Bronze Age people from Ireland had steppe ancestry and R1b

From the paper:

We were able to deduce that Neolithic Ballynahatty had a dark hair shade (99.5% probability), most likely black (86.1% probability), and brown eyes (97.3% probability) (46). Bronze Age Rathlin1 probably had a light hair shade (61.4%) and brown eyes (64.3%). However, each Rathlin genome possessed indication of at least one copy of a haplotype associated with blue eye color in the HERC2/OCA2 region.

and:

Third, we followed the methods described in Haak et al. (9), which use a collection of outgroup populations, to estimate the mixture proportions of three different sources, Linearbandkeramik (Early Neolithic; 35 ± 6%), Loschbour (WHG; 26 ± 12%), and Yamnaya (39 ± 8%), in the total Irish Bronze Age group. These three approaches give an overlapping estimate of ∼32% Yamnaya ancestry.

PNAS doi: 10.1073/pnas.1518445113

Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome

Lara M. Cassidy, Rui Martiniano et al.

The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343–3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter–gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026–1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.

Link

Natural selection and ancient European DNA

A new preprint on the bioRxiv studies the same data as the recent Haak et al. paper, but focuses on natural selection in Europe. Until recently, selection could only be studied by looking at modern populations, but since selection is genetic change over time effected by the environment, it's possible that studies like this will be the norm in the future.

The new study seems to confirm the results of Wilde et al. on steppe groups, as the Yamnaya had a very low frequency of the HERC2 derived "blue eye" allele and a lower frequency of the SLC45A2 "light skin" allele than any modern Europeans. The Yamnaya seem to have been fixed for the other SLC24A5 "light skin" allele which seems to have been at high frequency in all ancient groups save the "Western Hunter Gatherers".

It seems that light pigmentation traits had already existed in pre-Indo-European Europeans (both farmers and hunter-gatherers) and so long-standing philological attempts to correlate them with the arrival of light-pigmented Indo-Europeans from the steppe (or indeed anywhere), and to contrast them with darker pre-Indo-European inhabitants of Europe were misguided. If anything, it seems that the "fairest of them all" were the Scandinavian hunter-gatherers, and a combination of light/dark pigmentation was also present in Neolithic farmers and Western Hunter Gatherers in various combinations.

It also seems that both the theory that lactose tolerance started with LBK farmers and the theory that it came to Europe from milk-drinking steppe Indo-Europeans were wrong, as this trait seems to be altogether absent in European hunter-gatherers, farmers, and Yamnaya, and make a very timid appearance in the Late neolithic/Bronze Age before shooting up in frequency to the present.

Another new development is the ability to predict "genetic height" from ancient DNA. I think this may be a little bit superfluous as you can predict "actual height" by measuring long bone lengths. On the other hand, actualized height depends not only on genetics but also on diet, disease, etc., so it's useful to look at genetic changes in such polygenic traits directly.

A big surprise was the presence of the derived EDAR allele in Swedish hunter-gatherers. This allele is very rare in modern Europeans and seems to have pleiotropic effects in East Asians. This raises the question why this allele (that was so successful in East Asians), never "took hold" in Europeans. One possibility is that it never provided an advantage to Europeans (I don't think anyone really knows what it's actually good for). Another is that Swedish hunter-gatherers simply didn't contribute much ancestry to modern Europeans and so the allele never got the chance to rise in frequency by much.

bioRxiv http://dx.doi.org/10.1101/016477

Eight thousand years of natural selection in Europe

Iain Mathieson et al.

The arrival of farming in Europe beginning around 8,500 years ago required adaptation to new environments, pathogens, diets, and social organizations. While evidence of natural selection can be revealed by studying patterns of genetic variation in present-day people, these pattern are only indirect echoes of past events, and provide little information about where and when selection occurred. Ancient DNA makes it possible to examine populations as they were before, during and after adaptation events, and thus to reveal the tempo and mode of selection. Here we report the first genome-wide scan for selection using ancient DNA, based on 83 human samples from Holocene Europe analyzed at over 300,000 positions. We find five genome-wide signals of selection, at loci associated with diet and pigmentation. Surprisingly in light of suggestions of selection on immune traits associated with the advent of agriculture and denser living conditions, we find no strong sweeps associated with immunological phenotypes. We also report a scan for selection for complex traits, and find two signals of selection on height: for short stature in Iberia after the arrival of agriculture, and for tall stature on the Pontic-Caspian steppe earlier than 5,000 years ago. A surprise is that in Scandinavian hunter-gatherers living around 8,000 years ago, there is a high frequency of the derived allele at the EDAR gene that is the strongest known signal of selection in East Asians and that is thought to have arisen in East Asia. These results document the power of ancient DNA to reveal features of past adaptation that could not be understood from analyses of present-day people.

Link (pdf)

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

Brown-skinned, blue-eyed, Y-haplogroup C-bearing European hunter-gatherer from Spain (Olalde et al. 2014)

There is nothing like a little ancient DNA weirdness to start off 2014, which promises to be as exciting as 2013 was.

The new study La Brana 1 identifies it as ancestral in the SLC24A5 locus in which virtually all Europeans are derived. This comes in the heels of the Loschbour preprint which identified that sample from Luxembourg as also being ancestral. Taken together, it's now clear that hunter-gatherers from Mesolithic Western Europe were brown.

Curiously, it now seems that both Europe and India were (in part) inhabited by brown people and became lighter by a process of admixture + selection. The process went "all the way" in Europe, but a cline of pigmentation was sustained in India.

The other finding (not mentioned in the abstract) is that La Brana 1 belonged to Y-haplogroup C6! This is a low-frequency European clade of haplogroup C. So now, we have evidence that haplogroup C is not eastern Eurasian (as the presence of its subclades in Australia, India, East Asia, and the Americas might suggest), but a pan-Eurasian entity. It remains to be seen whether this C-in-Europe can be pushed further back in time, but finding it in Mesolithic Iberia reduces the chance that it's some random eastern Eurasian who made it to the outskirts of Europe recently.

Finally, La Brana 1 has derived alleles at loci associated with pathogen resistance. This might be important, because a common hypothesis is that Europeans developed this type of resistance during the Neolithic as they started interacting with the pathogens of domesticated species and started living in less-hygienic higher-density settlements.


Nature (2014) doi:10.1038/nature12960

Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European

Iñigo Olalde et al.

Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe1, 2, 3. The adoption of farming, stock breeding and sedentary societies during the Neolithic may have resulted in adaptive changes in genes associated with immunity and diet4. However, the limited data available from earlier hunter-gatherers preclude an understanding of the selective processes associated with this crucial transition to agriculture in recent human evolution. Here we sequence an approximately 7,000-year-old Mesolithic skeleton discovered at the La Braña-Arintero site in León, Spain, to retrieve a complete pre-agricultural European human genome. Analysis of this genome in the context of other ancient samples suggests the existence of a common ancient genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic. The La Braña individual carries ancestral alleles in several skin pigmentation genes, suggesting that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Moreover, we provide evidence that a significant number of derived, putatively adaptive variants associated with pathogen resistance in modern Europeans were already present in this hunter-gatherer.

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

How people get blue eyes

Genome-wide association studies can uncover links between genetic variants and phenotypes, even in the absence of any knowledge of how these links come about. All it takes is to make a statistical case linking genetic variation with the recorded phenotypic information.

This is somewhat unsatisfactory for a couple of reasons. First, we would like to know how cause and effect works, rather than simply observe that it does. Why do some people with certain genetic alleles have blue eyes?

Second, such functional studies allow us to predict phenotypes from genotypes. A great number of genetic mutations may cause particular phenotypes, and we are only able to discover associations between a subset of them that happens to exist in a population. Developing knowledge about function, rather than just statistical association, may help us in the future to infer the phenotypes of individuals from the deep past for which all non-osteological traces of phenotype have vanished, and may have been affected by genetic variants that are now extinct.

Many human traits are governed by a great number of genes, either through additive effects, or through complex interactions. Eye color is an example of a particular trait the genetic underpinnings of which in Caucasoids (other races have eyes that are uniformly brown) have been known for a while. Now a new study shows precisely how genetic mutations disrupt the formation of pigment in melanocytes, resulting in light-pigmented irides.


Genome Res doi:10.1101/gr.128652.111

HERC2 rs12913832 modulates human pigmentation by attenuating chromatin loop formation between a long-range enhancer and the OCA2 promoter

Mijke Visser et al.

Pigmentation of skin, eye and hair reflects some of the most evident common phenotypes in humans. Several candidate genes for human pigmentation are identified, and the SNP rs12913832 has strong statistical association with human pigmentation. It is located within an intron of the non-pigment gene HERC2, 21 kb upstream of the pigment gene OCA2, and the region surrounding rs12913832 is highly conserved among animal species. However, the exact functional role of HERC2 rs12913832 in human pigmentation is unknown. Here we demonstrate that the HERC2 rs12913832 region functions as an enhancer regulating OCA2 transcription. In darkly pigmented human melanocytes carrying the rs12913832 T-allele, we detected binding of the transcription factors HLTF, LEF1 and MITF to the HERC2 rs12913832 enhancer, and a long-range chromatin loop between this enhancer and the OCA2 promoter which leads to elevated OCA2 expression. In contrast, in lightly pigmented melanocytes carrying the rs12913832 C-allele, chromatin-loop formation, transcription factor recruitment and OCA2 expression are all reduced. Hence, we demonstrate that allelic variation of a common non-coding SNP located in a distal regulatory element not only disrupts the regulatory potential of this element but also affects its interaction with the relevant promoter. We provide the key mechanistic insight that allele-dependent differences in chromatin-loop formation (i.e. structural differences in the folding of gene loci) results in differences in allelic gene expression that affects common phenotypic traits. This concept is highly relevant for future studies aiming to unveil the functional basis of genetically-determined phenotypes including diseases.

Link

Y chromosome and mtDNA of Louis XVI of France (?)

From the paper:

After the execution of Louis XVI in January 21st, 1793, eyewitnesses stated that many people from the crowd dipped their handkerchiefs in the king’s blood and kept these objects as mementos [8]. An Italian family has owned for more than a hundred years – as demonstrated by a letter addressed to the director of the Muse/ e Carnavalet in Paris, January 31st, 1900 – a dessicated gourd that presumably contained one of these handkerchiefs.

The mtDNA results:

the majority of the cloned sequences (87%) showed a rare N1b haplotype, with the substitutions 16093C-16145A-16176(G)-16223T. The same results were found in Bologna by direct sequencing, along with another substitution (16390G), not included in the amplicon generated in Barcelona. The haplotype found at the mtDNA HVR2(73G, 151T, 152C, 189G, 194T, 195C, 263G and 315.1C), is consistent with the N1b haplotype from the HVR1, although the substitutions 151T, 189G and 194T are not described in the current N1b dataset lineages. We interpret these three substitutions as additional, undescribed modifications of a N1b haplotype.

The Y-chromosome STR markers:

A ysearch query reveals a handful of distant (3 off in 9 markers) matches ranging from Anatolia to Scotland. Likewise yhrd turns up no matches using either the full or restricted panel, but a 1-off match with DYS389II-29 in the restricted panel in Marche, Italy.

Wikipedia tells me that Louis XVI's patrilineage goes all the way to Robert the Strong, and his matrilineage to Catherine of Mayenne.

One would think that a 1,000-year long line of kings and nobles would have left enough side branches and bastards along the way to register a few hits on the European map. Perhaps, that's a reason to stress the "presumed" in the paper's title. On the other hand, I find it interesting that the presumptive haplogroup of Louis XVI was G2a, the same as 2 of 5 warriors from Merovingian Bavaria (7th c. AD).

There is a way to authenticate the results, as the authors note:

At present it is not possible to prove genetically that the sample really belongs to the king Louis XVI. One possibility would be to extract a new sample from the dry heart attributed to the Dauphin Louis XVII, son of Louis XVI, preserved at the Basilique Saint-Denis in Paris, and compare both Y-chromosome profiles. Owing to the fact that the Y-chromosome profile found is not present in our current genetic databases such as YHRD, a potential match would directly authenticate the studied blood sample.

Forensic Sci Int Genet. 2010 Oct 10. [Epub ahead of print]

Genetic analysis of the presumptive blood from Louis XVI, king of France.

Lalueza-Fox C, Gigli E, Bini C, Calafell F, Luiselli D, Pelotti S, Pettener D.

Institut de Biologia Evolutiva, CSIC-UPF, Dr. Aiguader 88, 08003 Barcelona, Spain.

Abstract
A text on a pyrographically decorated gourd dated to 1793 explains that it contains a handkerchief dipped with the blood of Louis XVI, king of France, after his execution. Biochemical analyses confirmed that the material contained within the gourd was blood. The mitochondrial DNA (mtDNA) hypervariable region 1 (HVR1) and 2 (HVR2), the Y-chromosome STR profile, some autosomal STR markers and a SNP in HERC2 gene associated to blue eyes, were retrieved, and some results independently replicated in two different laboratories. The uncommon mtDNA sequence retrieved can be attributed to a N1b haplotype, while the novel Y-chromosome haplotype belongs to haplogroup G2a. The HERC2 gene showed that the subject analyzed was a heterozygote, which is compatible with a blue-eyed person, as king Louis XVI was. To confirm the identity of the subject, an analysis of the dried heart of his son, Louis XVII, could be undertaken.

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.

Link

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.

Link

European population structure with 300K SNPs and 6,000 individuals

This is a nice paper on European population structure with a large number of SNPs, which comes at the heels of some earlier studies:

• Genetic structure in Northern Europe with 250K SNPs
• Geography and Genetic structure in Europe (again)
• 500K SNP Europe-wide study of genetic structure

Some observations:

• In this study the first principal component of variation is along an east-west axis, rather than north-south as in previous studies. This is due to the limited number of southern European populations, and the great number of populations along an east-west axis from Spain to Russia. As I have mentioned before, the results of a principal components analysis are dataset-dependent.
• The nice technique of this paper is to infer the ancestry of an unknown sample (which could be perhaps a forensic case or customer of an ancestry analysis test) using only summary statistics. Imagine that you have 1,000 individuals from different populations, and want to guess the ancestry of an unknown test case. You could go about doing a full STRUCTURE run using the 1,001 individuals, or you could exploit the information garnered from an analysis of the 1,000 individuals (a PCA analysis in this case) to test the 1,001th individual. This is much faster and convenient, since the full STRUCTURE run is very time consuming.

In the substantive part of the paper, there are many results which you can read for yourselves (it's free to view), but I will comment on just two, which are related to what I wrote previously, rgarding a previous study:

Some ethnic groups are clearly distinguishable from each other (e.g. Swedes vs. Spaniards); some groups are partitioned into fairly disjoint sets (Spain I vs. Catalans in Spain II); others mutually overlap (e.g., British and Irish); while others overlap asymetrically (e.g., some former Yugoslavs in the Greek cluster, but not vice versa).

In this paper, the authors did a systematic study of the "ethnic distinctiveness" of their samples. In a first experiment, they used 80% of their data to identify the features of the various populations (e.g., Germans or Spaniards), and then tried to guess the origin of the remaining 20%:
It is clear that some nations appear to be distinct. For example, most test Spaniards (94.5%) are correctly guessed as Spaniards, with some (5.5%) guessed as French. Of course, this distinctiveness would be reduced if further populations (e.g. the Portuguese) were added to the analysis. More strongly, 99.1% of Norwegians are guessed correctly as Norwegians.

Other nations appear to be less distinct. For example, only 45.3% of Slovaks are guessed as Slovaks with most of the remaining ones guessed as Czechs (25%) or Hungarians (22%).

In some cases there is asymmetry of affiliation. For example, no Belgians are guessed as Germans but 10.2% of Germans are guessed as Belgians. Similarly 9.9% of Swedes are guessed as Norwegians, but only 1% of Norwegians are guessed as Swedes. While each case needs to be addressed individually, this observation is consistent with historical asymmetry in immigration patterns or ethnic identity formation. So, while e.g., the bulk of Germans (64.4%) are guessed correctly, sizeable minorities are guessed as Czechs, Belgians, or Scandinavians.

I would speculate that large central European countries have historically (both due to prestige or geographical position) absorbed more diverse populations from neighboring nations, while smaller peripheral countries have mostly acted as sources of population, reserving their own genetic distinctiveness.

In a second experiment the authors guessed the origin of individuals, but excluding the country from which they actually originated.

Once again, it is clear that members of particular nations can mostly be mistaken for members of their closest neighbors. Almost all Spaniards are guessed as French; French mostly as Belgians but with sizable Spanish and UK minorities; UK as Belgians but with sizable French minorities; Norwegians mostly as Swedes but with some UK; Swedes mainly as Germans but many as Norwegians; most Poles as Russians, but some Slovaks or Czechs, and so on.

The importance of these results can't be underestimated. While it can be argued that some ethnic groups are spuriously distinctive only due to insufficient sampling of the geographical continuum, it is more difficult to do this for others. For example, it is now possible to identify particular ethnic groups, e.g., Norwegians, with great accuracy from DNA.

More markers and more populations will doubtlessly enhance our ability to distinguish European nations using DNA. But perfect accuracy is unlikely; in most European nations there are probably minorities which -for historical reasons- allied themselves with one country or political entity even though they were ultimately of different genetic background than the majority population of that entity.

Nonetheless, at a time when -due to a sort of mental hysteresis- proclamations that "races are social constructs" are still routinely made, the discovery that not only races, but even closely related ethnic groups (e.g. Norwegians and Swedes) can be distinguished with greater than 90% accuracy, serves to illustrate the scientific irrelevance of the ethnic nihilists and the affirmation that nations are, at least in part, genetic entities.

European Journal of Human Genetics (2008) 16, 1413–1429; doi:10.1038/ejhg.2008.210

Investigation of the fine structure of European populations with applications to disease association studies

Simon C Heath et al.

Abstract

An investigation into fine-scale European population structure was carried out using high-density genetic variation on nearly 6000 individuals originating from across Europe. The individuals were collected as control samples and were genotyped with more than 300 000 SNPs in genome-wide association studies using the Illumina Infinium platform. A major East–West gradient from Russian (Moscow) samples to Spanish samples was identified as the first principal component (PC) of the genetic diversity. The second PC identified a North–South gradient from Norway and Sweden to Romania and Spain. Variation of frequencies at markers in three separate genomic regions, surrounding LCT, HLA and HERC2, were strongly associated with this gradient. The next 18 PCs also accounted for a significant proportion of genetic diversity observed in the sample. We present a method to predict the ethnic origin of samples by comparing the sample genotypes with those from a reference set of samples of known origin. These predictions can be performed using just summary information on the known samples, and individual genotype data are not required. We discuss issues raised by these data and analyses for association studies including the matching of case-only cohorts to appropriate pre-collected control samples for genome-wide association studies.

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More ASHG 2008 abstracts

The previous batch is here.

Analysis of East Asia Genetic Substructure: Population Differentiation and PCA Clusters Correlate with Geographic Distribution

Accounting for genetic substructure within European populations has been important in reducing type 1 errors in genetic studies of complex disease. As efforts to understand complex genetic disease are expanded to other continental populations an understanding of genetic substructure within these continents will be useful in design and execution of association tests. In this study, population differentiation(Fst) and Principal Components Analyses(PCA) are examined using >200K genotypes from multiple populations of East Asian ancestry(total 298 subjects). The population groups included those from the Human Genome Diversity Panel[Cambodian(CAMB), Yi, Daur, Mongolian(MGL), Lahu, Dai, Hezhen, Miaozu, Naxi, Oroqen, She, Tu, Tujia, Naxi, and Xibo], HapMap(CHB and JPT), and East Asian or East Asian American subjects of Vietnamese(VIET), Korean(KOR), Filipino(FIL) and Chinese ancestry. Paired Fst(Wei and Cockerham) showed close relationships between CHB and several large East Asian population groups(CHB/KOR, 0.0019; CHB/JPT, 00651; CHB/VIET, 0.0065) with larger separation with FIL(CHB/FIL, 0.014). Low levels of differentiation were also observed between DAI and VIET(0.0045) and between VIET and CAMB(0.0062). Similarly, small Fsts were observed among different presumed Han Chinese populations originating in different regions of mainland of China and Taiwan. For example, the four For PCA, the first two PCs showed a pattern of relationships that closely followed the geographic distribution of the different East Asian populations.corner groups were JPT, FIL, CAMB and MGL with the CHB forming the center group, and KOR was between CHB and JPT. Other small ethnic groups were also in rough geographic correlation with their putative origins. These studies have also enabled the selection of a subset of East Asian substructure ancestry informative markers(EASTASAIMS) that may be useful for future genetic association studies in reducing type 1 errors and in identifying homogeneous groups.

Worldwide Population Structure using SNP Microarray Genotyping

We genotyped 348 individuals sampled from 24 populations world-wide using the Affymetrix 250k NspI microarray chip. For context, we added matching genotypes from 210 HapMap individuals for a total of 250,823 loci genotyped in 543 individuals from 28 populations. We included populations from India and Daghestan to provide detail between the genetic poles of Western Europe, East Asia, and sub-Sahara Africa. With so many markers, principal components analyses reveal genetic differentiation between almost all identified populations in our sample. Northern and southern European populations (FST = 0.004, p <0.01) are statistically distinguishable, as are upper and lower caste groups in India (FST = 0.005, p <0.01). All individuals are accurately classified into continental groups, and even between closely-related populations, genetic- and self-classifications conflict for only a minority of individuals (e.g. ~2% between upper and lower Indian castes; k-means clustering.) As expected, the HapMap CHB+JPT, CEU, and YRI samples are most similar to our east Asian, west European, and African samples, respectively. The HapMap CEU samples and our northern European ancestry samples were both collected from Utah. Although individual samples cannot be reliably classified into their collection of origin, the groups are statistically distinguishable despite their high similarity (FST = 0.0005, n.s.). Our Japanese group is also statistically distinguishable from the HapMap JPT group (FST = 0.006, p <0.01), and in this comparison, most samples can be correctly classified. With such large numbers of genotypes, significant differences can be found even between very similar population samplings. Our results provide guidelines for researchers in selecting suitable control populations for case-control studies.

Frequency distribution and selection in 4 pigmentation genes in Europe

Pigmentation is one of the more obvious forms of variation in humans, particularly in Europeans where one sees more within group variation in hair and eye pigmentation than in the rest of the world. We studied 4 genes (SLC24A5, SLC45A2, OCA2 and MC1R) that are believed to contribute to the pigment phenotypes in Europeans. SLC24A5 has a single functional variant that leads to lighter skin pigmentation. Data on 83 populations worldwide (including 55 from our lab) show the variant (at rs1426654) has almost reached fixation in Europe, Southwest Asia, and North Africa, has moderate to high frequencies (.2-.9) throughout Central Asia, and has frequencies of .1-.3 in East and South Africa. The variant is essentially absent elsewhere. SLC45A2 also has a single functional variant (at rs16891982) associated with light skin pigmentation in Europe. Data on 84 populations worldwide show the light skin allele is nearly fixed in Northern Europe but has lower frequencies in Southern Europe, the Middle East and Northern Africa. In Central Asia the frequency of the SLC45A2 variant declines more quickly than the SLC24A5 variant. It is absent in both East and South Africa. In OCA2 we typed 4 SNPs (rs4778138, rs4778241, rs7495174, rs12913832) with a haplotype associated with blue eyes in Europeans. This haplotype shows a Southeastern to Northwestern pattern in Europe with frequencies of .25 (.05 homozygous) in the Adygei to .85 (.75 homozygous) in the Danes. In MC1R we typed 5 SNPs (rs3212345, rs3212357, rs3212363, C_25958294_10, rs7191944) that cover the entire MC1R gene and found a predominantly European haplotype that ranges in frequency from .35 to .65 in Europe, reaching its highest levels in Southwest Asia and Northwestern Europe. Extended Haplotype Heterozygosity (EHH) and normalized Haplosimilarity (nHS) show evidence of selection at SLC24A5 in not only our European and Southwest Asian populations but also our East African populations. Neither SLC45A2 or OCA2 showed evidence of selection in either test. MC1R did not show evidence of selection for our European specific haplotype but we did see some evidence both upstream and downstream in our nHS test in Europe.

Using principal components analysis to identify candidate genes for natural selection.

Genetic markers that differentiate populations are excellent candidates for natural selection due to local adaptation, and may shed light into physiological pathways that underlie disorders with varying frequencies around the world. Principal Components Analysis (PCA) has emerged as a powerful tool for the characterization and analysis of the structure of genomewide datasets. In prior work, we described an algorithm that can be used to select small subsets of genetic markers (SNPs) that correlate well with population structure, as captured by PCA. Our method can be used to detect SNPs that differentiate individuals from different geographic regions, or even neighboring subpopulations. We set out to explore the nature and properties of the genes where population-differentiating SNPs reside, by analyzing the publicly available Human Genome Diversity Panel dataset (650,000 SNPs for 1,043 individuals, 51 populations). Applying our SNP selection algorithms, we chose small subsets of SNPs that almost perfectly reproduce worldwide population structure as identified by PCA. We determined SNP panels both for population differentiation within seven geographic regions, as well as around the globe. We then explored the hypothesis that the selected SNPs attained their current worldwide allele frequency patterns as a response to the pressure of natural selection. Comparing our lists to recently published reports, we found a significant overlap with other genomewide scans for selection, thus validating our hypothesis. For example, EDAR (involved in the development of hair follicles) harbors the most differentiating SNPs in our world-wide panels. SNPs located in genes that are involved in skin and eye pigmentation (OCA2, MYO5C, HERC1, HERC2) are also among the top population differentiating markers. In East Asia, SNPs residing at the ADH cluster appear among the most important SNPs for population structure, while, in Europe, the same is true for genes that are involved in immune response to pathogens (CR1, DUOX2, TLR, and HLA). Finally, a comprehensive gene ontology analysis is presented.

New alleles for hair and skin pigmentation

Gnxp points me to this new paper on hair and skin color pigmentation alleles.

PLoS Genet 4(5): e1000074. doi:10.1371/journal.pgen.1000074

A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation

Jiali Han et al.

Abstract

We conducted a multi-stage genome-wide association study of natural hair color in more than 10,000 men and women of European ancestry from the United States and Australia. An initial analysis of 528,173 single nucleotide polymorphisms (SNPs) genotyped on 2,287 women identified IRF4 and SLC24A4 as loci highly associated with hair color, along with three other regions encompassing known pigmentation genes. We confirmed these associations in 7,028 individuals from three additional studies. Across these four studies, SLC24A4 rs12896399 and IRF4 rs12203592 showed strong associations with hair color, with p = 6.0×10⁻⁶² and p = 7.46×10⁻¹²⁷, respectively. The IRF4 SNP was also associated with skin color (p = 6.2×10⁻¹⁴), eye color (p = 6.1×10⁻¹³), and skin tanning response to sunlight (p = 3.9×10⁻⁸⁹). A multivariable analysis pooling data from the initial GWAS and an additional 1,440 individuals suggested that the association between rs12203592 and hair color was independent of rs1540771, a SNP between the IRF4 and EXOC2 genes previously found to be associated with hair color. After adjustment for rs12203592, the association between rs1540771 and hair color was not significant (p = 0.52). One variant in the MATP gene was associated with hair color. A variant in the HERC2 gene upstream of the OCA2 gene showed the strongest and independent association with hair color compared with other SNPs in this region, including three previously reported SNPs. The signals detected in a region around the MC1R gene were explained by MC1R red hair color alleles. Our results suggest that the IRF4 and SLC24A4 loci are associated with human hair color and skin pigmentation.

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Human eye color news

From the first paper, the frequency of HERC2 rs916977 superimposed on an iris color map (sadly taken from a 1965 reference):


The American Journal of Human Genetics,
doi:10.1016/j.ajhg.2007.10.003

Three Genome-wide Association Studies and a Linkage Analysis Identify HERC2 as a Human Iris Color Gene

Manfred Kayser et al.

Abstract

Human iris color was one of the first traits for which Mendelian segregation was established. To date, the genetics of iris color is still not fully understood and is of interest, particularly in view of forensic applications. In three independent genome-wide association (GWA) studies of a total of 1406 persons and a genome-wide linkage study of 1292 relatives, all from the Netherlands, we found that the 15q13.1 region is the predominant region involved in human iris color. There were no other regions showing consistent genome-wide evidence for association and linkage to iris color. Single nucleotide polymorphisms (SNPs) in the HERC2 gene and, to a lesser extent, in the neighboring OCA2 gene were independently associated to iris color variation. OCA2 has been implicated in iris color previously. A replication study within two populations confirmed that the HERC2 gene is a new and significant determinant of human iris color variation, in addition to OCA2. Furthermore, HERC2 rs916977 showed a clinal allele distribution across 23 European populations, which was significantly correlated to iris color variation. We suggest that genetic variants regulating expression of the OCA2 gene exist in the HERC2 gene or, alternatively, within the 11.7 kb of sequence between OCA2 and HERC2, and that most iris color variation in Europeans is explained by those two genes. Testing markers in the HERC2-OCA2 region may be useful in forensic applications to predict eye color phenotypes of unknown persons of European genetic origin.

Link

The American Journal of Human Genetics,
doi:10.1016/j.ajhg.2007.11.005

A Single SNP in an Evolutionary Conserved Region within Intron 86 of the HERC2 Gene Determines Human Blue-Brown Eye Color

Richard A. Sturm et al.

Abstract

We have previously demonstrated that haplotypes of three single nucleotide polymorphisms (SNPs) within the first intron of the OCA2 gene are extremely strongly associated with variation in human eye color. In the present work, we describe additional fine association mapping of eye color SNPs in the intergenic region upstream of OCA2 and within the neighboring HERC2 (hect domain and RLD2) gene. We screened an additional 92 SNPs in 300–3000 European individuals and found that a single SNP in intron 86 of HERC2, rs12913832, predicted eye color significantly better (ordinal logistic regression R2 = 0.68, association LOD = 444) than our previous best OCA2 haplotype. Comparison of sequence alignments of multiple species showed that this SNP lies in the center of a short highly conserved sequence and that the blue-eye-associated allele (frequency 78%) breaks up this conserved sequence, part of which forms a consensus binding site for the helicase-like transcription factor (HLTF). We were also able to demonstrate the OCA2 R419Q, rs1800407, coding SNP acts as a penetrance modifier of this new HERC2 SNP for eye color, and somewhat independently, of melanoma risk. We conclude that the conserved region around rs12913832 represents a regulatory region controlling constitutive expression of OCA2 and that the C allele at rs12913832 leads to decreased expression of OCA2, particularly within iris melanocytes, which we postulate to be the ultimate cause of blue eye color.

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