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Monday, January 27, 2014

Mesolithic genome from Spain reveals markers for blue eyes, dark skin and Y-haplogroup C6

Nature today published the eagerly awaited paper on the complete genome of La Brana 1: Olalde et al. 2014. The relatively high quality (3.4x coverage) genome suggests that the Iberian hunter-gatherer had blue eyes, dark hair and deep brown skin.

Moreover, he was probably lactose intolerant (in other words, unlike most Europeans today, he couldn't drink milk as an adult), and his Y-chromosome belonged to the European-specific, but extremely rare, haplogroup C6 (aka. C-V20), and mtDNA to haplogroup U5b2c1, which again is a European-specific marker. Below is an artist's impression of his mug (courtesy of CSIC), and below that the paper abstract.

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.

Indeed, the pigmentation traits are basically the same as those of Loschbour, a Mesolithic genome from Luxembourg, featured recently in the groundbreaking Lazaridis et al. preprint (see here). So we can already speculate with some confidence that this was a common, and perhaps dominant, trait combination among European hunter-gatherers.

However, early European farmers, whose ancestors almost certainly migrated to Europe from the Near East during the Neolithic, probably had somewhat different pigmentation traits. We know this because a 7,500 year-old Linearbandkeramik (LBK) farmer genome from Stuttgart, Germany, also featured in Lazaridis et al., showed markers for brown eyes, dark hair, and relatively light skin.

So as things stand, it appears that Europeans only acquired their present coloring, including pale skin and a high incidence of light eyes, relatively recently, well after the hunter-gatherers and farmers began mixing, and their hybrid DNA had time to go through some really powerful selective sweeps. These sweeps were possibly in part a reaction to the Neolithic diet, rich in carbohydrates but poor in vitamin D, amongst other things. Vitamin D doesn't have to be acquired from food because the body can synthesize it from the sun, but this is done more effectively by people with fair skin, giving them an advantage, especially in places like Europe, which has fairly long winters and lots of cloud cover.

But perhaps this isn't the full story, and present-day European pigmentation traits are also sourced from a late migration into Europe of a prevailingly blond people from somewhere in what is now Russia?

This might sound far fetched, but during the middle Bronze Age the Eurasian steppe was home to the Andronovo culture, with archeological links to earlier cultures in what is now southern Russia. Based on the DNA of Andronovo nomads from Kurgans in South Siberia, it seems they had fair skin and a lot of blue eyes and blond hair (see here). They also overwhelmingly belonged to Y-chromosome haplogroup R1a1a, which is very common today in Central and Eastern Europe and also parts of Scandinavia. So it'll be interesting to see the pigmentation markers of Mesolithic Eastern Europeans and Central Asians when their genomes become available, probably in the not too distant future, and if they contributed any ancestry to present-day Europeans. Early indications are that they did, and I discussed that in my previous blog entry here.

Now, La Brana 1 and Loschbour were both classified as part of the West European Hunter-Gatherer (WHG) mata-population by Lazaridis et al., even though only a partial sequence from La Brana 1 was available at the time. As far as I can see, the results in Olalde et al. based on the complete genome don't contradict this classification, because they show that La Brana 1 is most similar to present-day Europeans from around the Baltic Sea, just like Loschbour. Note, for instance, the position of Swedes (SE) and Poles (PL) on the far right of these graphs, indicating inflated allele sharing between them and La Brana 1 relative to other Europeans.

But the paper also underlines the very close genetic relationship between La Brana 1 and the 24,000 year-old genome from Siberia known as MA-1, which was used as the proxy for the Ancient North Eurasian (ANE) ancestral component in Lazaridis et al. The authors' comments remind me of an earlier study based on ancient mtDNA data which argued that the region from Iberia to Central Siberia was home to a relatively homogeneous gene pool during the Mesolithic, with high frequencies of mtDNA haplogroups U2, U4 and U5 (see here). Please note, MA-1 belonged to Y-haplogroup R*, but carried mtDNA haplogroup U*.

Outgroup f3 and D statistics (16,17), using different modern reference populations, support that Mal’ta is significantly closer to La Brana 1 than to Asians or modern Europeans (Extended Data Fig. 5 and Supplementary Information). These results suggest that despite the vast geographical distance and temporal span, La Brana 1 and Mal’ta share common genetic ancestry, indicating a genetic continuity in ancient western and central Eurasia. This observation matches findings of similar cultural artefacts across time and space in Upper Paleolithic western Eurasia and Siberia, particularly the presence of anthropomorphic ‘Venus’ figurines that have been recovered from several sites in Europe and Russia, including the Mal’ta site.

Unfortunately, I have to say that the main Principal Component Analysis (PCA) from the paper isn't as informative as it could have been, due to the large number of Finnish individuals included in the analysis. It's mostly a reflection of the recent population growth, founder effect and genetic drift among Finns, particularly those from eastern Finland. This is exactly the same problem that affected the PCA in Sánchez-Quinto et al. 2012, the paper that reported on the partial genomic sequences of La Brana 1 and 2 (see here).

Nevertheless, note that all of the non-Finnish Europeans more or less fall along the cline that runs from La Brana 1 to present-day Cypriots. This suggests that Europeans today are mostly the product of mixture, in varying degrees, between indigenous European hunter-gatherers, like La Brana 1 and Loschbour, and immigrant Neolithic farmers from the East Mediterranean. So it's a result that basically agrees with the findings of Lazaridis et al.

Interestingly, Loschbour and four other Mesolithic samples from Lazaridis et al. belonged to Y-chromosome haplogroup I, which is not at all closely related to C6. This hints at the presence of a diverse Y-chromosome gene pool in pre-Neolithic Europe, and indeed I'm still confident of seeing R1 and/or R1a among Mesolithic remains from Eastern Europe.

Even though the vast majority of haplogroup C clades are today specific to Eastern Asia, Oceania and the Americas, C6 has only been found among a handful of individuals from across Southern, Western and Central Europe, many of whom are listed at the FTDNA haplogroup C project (look for the V20+ results here). It's difficult to say when this marker or its ancestral lineage migrated to Europe, but C is one of the most basal human Y-chromosome clades, so it could represent the very first Anatomically Modern Human (AMH) wave into Europe, which actually isn't a new concept (see Scozzari et al. 2012).

The Olalde et al. paper includes a lot more information than I'm willing to cover in this blog entry. If you don't have access to the main report, please note that the extended and supplementary data are very detailed and open access.


Olalde et al., Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European, Nature (2014), doi:10.1038/nature12960


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About Time said...

From the study: "All individuals were asked to fill in a questionnaire that included basic information, such as gender and age as well as data concerning eye and hair pigmentation phenotype."

This really makes me question these frequency numbers, because people use the same term to classify different objective colors. Especially cross-culture. People classify their hair color in relation to people they see in their country, so an Irish person's concept of "blond" will be different than a Norwegian's or a Greek's (even with a provided color chart).

Don't forget, EEF is WHG plus Basal, so there is WHG "baked in" everywhere in Europe, in case some of these pigment changes go back to WHG.

Also, it's possible blondism was popular in just one branch of EEF (not all). Like Funnelbeaker, but not in other EEF branches. Remember, EEF is pretty old (old enough to have local variants for visual traits).

Eduardo Pinto said...

There's a downloadable app right at the bottom called Interactive HIrisPlex prediction tool for hair and eye colour. You'll have to browse through your raw data and fill the S2 table and then compare it against the samples used in the study, table S1 .

Fanty said...

Hmm.... by googling around I found something that I hadnt heard of before.
But it says, British scientists found it first and then Czechians found the same thing again. Eye color apears somewhat connected to facial shape.

The study was about who apears more "trustworthy". Browneyed or blue eyed humans. It was found that browneyed humans apeared more trustworthy... BUT... they found, that its not dependant on the eye color at all. If they photoshopped the eyecolor of people, the trustworthy rate did not change.

They found, that its the facial shape that caused this. And that there is an odd connection between eye color and facial shape, even in one population.

It says... blue eyed humans faces apear angry or condemnatory, even if one photoshops them brown eyes. Browned eyed persons faces apear happy or benevolent, even if one shoppes them blue eyes.... errr... what? cO

a) blue eyed females
b) average females
c) brown eyed females

d) blue eyed males
e) average males
f) brown eyed males

g) minimum trustworthy males
h) average males
i) maximum trustworthy males

Kristiina said...

Apparently, all details of the colour inheritance are not so clear. My parents have both brown eyes but both have blue eyed sisters or brothers. My eyes are kind of greenish brown and my daughters have blue eyes. The eye color predictor on Gedcom predicted that my eyes should be blue grey (the brown eye probability was c. 1%). I commented the result by saying that the prediction was totally wrong. Moreover, I understood that the skin colour is even a more complex issue than the eye colour.

Grey said...


"so, if blonde hair means WHG"

I think different people are arguing different things. I think red/dark hair and *light*, not necessarily blue, eyes are WHG with more blond/blue coming in with the IE.

(Also nb although IE (at least on the maps) looks like it is mostly in a big wedge from NE to SW there is also the secondary path down along the west coast of the Black Sea into Greece.

I think a lot of these alleles will have a de-pigmentation effect so Euros with East Asian de-pigmentation, or rather changed pigmentation, alleles can drop a notch in their coloring i.e. red hair to blonde with KITLG or grey eyes to blue with OCA2.

Your stats on Greeks, Poles, Irish support the contention of red hair and **light** eyes going together separately from blond/blue.

Matt said...

@ About Time - Neolithic faces are defined by two differences from hunter gatherers

- slightly lower robusticity - robusticity is a kind of common shape vector distinguishing faces which are larger relative to overall body and brainsize from faces which are smaller relative to body

- slightly different shape once lower robusticity is accounted for

An decrease of robusticity being due to farmers selecting less for the appearance of strength (or mechanical facial strength) that's kind of plausible (a "more face like face(?)" seems like an odd idea - who's to say a more robust shape topography doesn't make emotions clearer, etc.).

A shift towards the specific features? Probably not, my reasoning being that if this were the case, you'd see similar shifts in the independent agricultural hearths in East Asia, America and Papua New Guinea. Which we don't.

In terms of what Europeans prefer in terms of facial features, I think beautiful is probably low robusticity.

But low robusticity faces that aren't otherwise particularly stereotypically Neolithic, like the Magda Fracowiak that Davidski has posted up, probably aren't particularly dispreferred. Europeans, taken as a group on average, would generally probably would find pleasing would be a Neolithic-Mesolithic mix with low robusticity (cute French girls?).

About Time said...

@Matt, facial robusticity tends to hide expressions and project a more "mask-like" face. Also, historically known hunter cultures (like Iroquois) made a big point of not showing emotions (even under extreme duress), so this was favored in the culture.

Some examples:

To use the dog/wolf analogy, wolves avoid eye contact (and physical touching), because it can be a sign of aggression. Hunters were more wolf-like and maybe even co-evolved with wolves specifically (copying behavior or selecting for similar behavior). Dogs love eye contact and touching.

My concept is that the Basal split from all other Non-Africans is related to the OOA expansion into hostile/dangerous Neanderthal territory (maybe under duress - for all we know, Neanderthals were advancing near a place where Basals were living and tried to compete for the habitat or harm Basals).

We don't know what Basal looked like, but we can see what high EEF populations and actual Neolithic burials looked like. They looked "Mediterranean" in the cranio-facial sense (as far as we know, they were the lightest humans around at the time wrt skin pigmentation).

I think Basals were selected for more "face-like" or "ultra-human" faces, partly due to a need to distinguish "Friendlies" from "Hostiles (Neanderthals)" during the OOA range expansion. This could favor people who were instantly recognizable as Non-Neanderthal/Friendlies.

Same process could have worked in other Non-Africans, but it's less obvious because they all mixed with Neanderthals. I sort of imagine it's possible WHG co-existed with Basals throughout this big range expansion by the way (sort of co-evolution, with Basals the more timid/reclusive inner core of the "OOA wave" and WHG the more aggressive and expansionary outer perimeter).

I also think Basals/EEF were more empathetic societies with more density and social complexity than hunting bands. So faces that showed (1) kinship and (2) emotion + thought/intention were favored.

I think of images like these:

Hunters knew each other personally, so bonds were different and more individual/personal (less need to show "I am a Friendly" when meeting someone).

So all this speculation gives a couple of testable hypotheses:

(1) Basals had less Neanderthal admixture than other Non-Africans. This should also hold for EEF versus WHG for same reason.
(2) ANE/WHG/ENA had more Neanderthal admixture than Basal.

Some other observations: anatomists looking at some of the Kurgan burials noticed Neanderthaloid features, like orbital ridges, metopic suture, and pointed shape of the calotte (don't ask me what that means, just retyping from book - I posted more on another thread here). If Kurgan was more ANE, this could be the Neanderthal admixture in ANE (now testable, not just a strange theory).

szopeno said...

"The reason red hair was mentioned in people who had it is because it sticks out "

Or because it *was* true but isn't now.

Didn't red paint was one of the earliest known to humans? WHy not simply assume the warriors painted their hair read to look more awesome/threatening?

Kurti said...

Since I didn't had any other option how to ask, I will ask you here. Davidski I got recently my y and mtDNA results. I am R1a1a* according to 23andme, I don't fit into the R1a1a1/R1a1a2/R1a1a3/R1a1a4/R1a1a5 clusters. This is my position in the Haplogroup Tree.

What could that be? To which sub clade could I belong to?

D. Virens said...

There might be a linguistic issue with those ancient accounts. It can depend on what words were used for "red." It wasn't long ago that "red" in English included orange and pink and rusty-colored. Yes, Latin and Greek had words for "yellow," but blond hair usually has orangish hues in it, so it's possible that what we call "blond" today was regarded back then as falling within the range of "red" (Latin ruber, etc.).

MickeyCool30 said...

it said Brana skin was dark an assumption to me. yes he contaibed the alleles but what people are forgetting is his haplogroup is older in age so has older skin pigmentation gebes does means he looked like an african. infact his facial features as with all the others look European nothing likr modern Arabs or Africans. it found north europeanHG had fair skin and eyes but same as those of yamnaya culture and Tocharians related? or just developed similar features.? if they mixed with HG then farmers should have older HG female lines. problem is yamnaya if they were r1a and r1b and as farmers went to balkans why is there such low rates of r1 in balkans? they seem to have ignored these areas and bypassed them for spain - not very logical to me. the r1a found in central asia seems pale skinned and light eyed but in India dark eyed and hairy. same with R1b some areas its dark eyed others its blue eyed other factors are going on. same with C6 blue eyed yet elsewhere dark

MickeyCool30 said...

if MA-1 was closer to Brana then MA-1 being R and Brana being C6 were close surely yet many modern europeans are R1 seems confusing!

MickeyCool30 said...

i agree we dont know his skin tone its an assumption. but also how can MA-1 not be related to modern Europeans he was R haplogroup like most modern male europeans?

MickeyCool30 said...

they found farmers werent dark skinned but light only dark eyes and skin. but people are missing climatic changes. there was the younger dryas and then heavy forests. what was climate in the middle east or bear the black sea at these times. starvation was a possibility as people changed diets it might affect sime haplogroups not others etc... we assume all these groups were separate (a modern construct) we dont know! if HG maintained shared dna across vast differences which does make sense, they were co ordinated. i presume they shared infornation. what if europeans and eurasians constantly sgared dna and links and gradually changed. if Brana and MA-1 shared links then this is a huge distance along the way there must of been genetic sharing to maintain these links not these vastly different peoples who had different cultures. venus figures were found over vast distances. many people today can have light skin blue eyes but dark hair . e.g. in nirth europe dark hairy folk must of had sex with red and blond northern folk

MickeyCool30 said...

the hair and eye colour match ice age climatic conditions added to that a linguistic argument i saw (makes a lot of sense) sayd IE came in with agriculture from Black Sea but not a movement of people but people from Black sea came in earlier before agriculture

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