The Archaeogenetics of Europe

[sumskilz]

Studies on ancient DNA published over the past few years have shed considerable light on European prehistory. I'm about to post one of them, and point out some aspects I find interesting, but I don't see any reason to limit the thread to prehistory since these developments also change how we have to interpret ancient DNA from historical periods as well.

Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity (Brandt, Haak et al.)

Abstract: The processes that shaped modern European mitochondrial DNA (mtDNA) variation remain unclear. The initial peopling by Palaeolithic hunter-gatherers ~42,000 years ago and the immigration of Neolithic farmers into Europe ~8000 years ago appear to have played important roles but do not explain present-day mtDNA diversity. We generated mtDNA profiles of 364 individuals from prehistoric cultures in Central Europe to perform a chronological study, spanning the Early Neolithic to the Early Bronze Age (5500 to 1550 calibrated years before the common era). We used this transect through time to identify four marked shifts in genetic composition during the Neolithic period, revealing a key role for Late Neolithic cultures in shaping modern Central European genetic diversity.

Some of you may be familiar with the various material cultures of prehistoric Europe illustrated here:

Spoiler Alert, click show to read: 

There has been a lot of debate in archaeology regarding how much can be inferred from material culture. Does material culture reflect identity, and if so, how fluid is this identity anyway, does it reflect decent, assimilation, or borrowing, and to what extent? This study finds a pretty solid correlation between mtDNA lineages and migrations evidenced by material culture.

Here are the mtDNA lineages associated with each of the migrations and their relative occurrence in ancient populations (based on current data):

Spoiler Alert, click show to read: 

The process by which Europe adopted agriculture seems to have largely been one of demographic replacement, as farmers from the Near East replaced Mesolithic hunter-gatherers. In this case, we're talking about mtDNA lineages which are matrilineal. This is significant because generally speaking Y-DNA lineages are more fluid as lineages of male conquerors who establish themselves as a ruling class displace native lineages to some extent as they monopolize females at the expense of local males. For example, Mexican mtDNA lineages are about 90% native, whereas Y-DNA lineages are 65% European and only 30% native. This Neolithic replacement is also supported by autosomal DNA. There is no living European population today which is particularly similar to the original inhabitants of Europe. Interestingly there is a resurgence of some of the Mesolithic lineages of in the late Middle Neolithic. This could represent an integration of some hunter-gather holdouts into settled farming society (see below).

Here is a video synthesizing the study's finds with migrations implied by material culture:



On a related note:

2000 Years of Parallel Societies in Stone Age Central Europe (Bollongino et al.)

Abstract: Debate on the ancestry of Europeans centers on the interplay between Mesolithic foragers and Neolithic farmers. Foragers are generally believed to have disappeared shortly after the arrival of agriculture. To investigate the relation between foragers and farmers, we examined Mesolithic and Neolithic samples from the Blätterhöhle site. Mesolithic mitochondrial DNA sequences were typical of European foragers, whereas the Neolithic sample included additional lineages that are associated with early farmers. However, isotope analyses separate the Neolithic sample into two groups: one with an agriculturalist diet and one with a forager and freshwater fish diet, the latter carrying mitochondrial DNA sequences typical of Mesolithic hunter-gatherers. This indicates that the descendants of Mesolithic people maintained a foraging lifestyle in Central Europe for more than 2000 years after the arrival of farming societies.

A summery of the original cultural groupings of each lineage:

mtDNA haplogroups associated with Mesolithic hunter-gathers: U, U4, U5, U8

mtDNA haplogroups associated with Neolithic farmers from the Middle-East: N1a, T2, K, J, HV, V, W, X

mtDNA haplogroups associated with the Corded Ware Culture: I, U2, T1, R

mtDNA haplogroup H first appeared associated with the Bell Beaker Culture and seems to have originated in Iberia, it is downstream of HV.

On a side note, at least some of the Indo-European languages likely arrived with the Corded Ware culture.

EDIT: I'll post more studies when I have a chance. Feel free to add studies you've come across, ask questions, or pose relevant speculations.

EDIT2: Here is a plot of some ancient autosomal DNA (mostly from Scandinavia) compared to modern populations:

Spoiler Alert, click show to read: 

This is from Skoglund, Pontus, et al. I've included it to back up my assertion that there are no modern populations similar to Mesolithic hunter-gatherers, although you can see who is closest. Note the similarity between Neolithic Scandinavian farmers and Basques.

[G-Megas-Doux]

Haplogroup X is fairly interesting in that it has a large divergence around the world as to where it is located and in which population but is quite small in terms of global numbers.

[sumskilz]

Haplogroup X is fairly interesting in that it has a large divergence around the world as to where it is located and in which population but is quite small in terms of global numbers.

The distribution of X, along with the distribution of Y-DNA Haplogroup R, has been argued to support the Solutrean hypothesis that North America was first populated via Europe.

It might look plausible when you see these:

Spoiler Alert, click show to read: 

But Stanford and Bradley don't really know what they're talking about when it comes to genetics. The geographic source of a haplogroup is not where it's most prevalent, because that could be founder's effect, it's actually where it's most diverse. More diversity of subclades means that the type has been in the population longer since it has had longer to diversify. The North American and European versions of these haplogroups represent different branches of groups that probably have their origins in the Middle-East. Not to mention, that the North American versions were probably in North America before the other branches even arrived in Europe.

R was found in 24,000 year old remains from Siberia in an individual whose autosomal DNA is intermediate between modern Europeans and Native Americans, but not particularly similar to any living population:

Spoiler Alert, click show to read: 

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans (Raghavan, Skoglund et al.)

Haplogroup X (mtDNA) is most diverse in the Middle-East, particularly among Druze who have been endogamous for a thousand years and so are more representative of the ancient population genetics of the region than most.

There is a question as to how selected (evolutionarily speaking) these haplogroups are. Why is mtDNA X at such a low frequency? How did just one to three men father most of Western Europe?

Abstract:

Background
Patterns of genetic variation in a population carry information about the prehistory of the population, and for the human Y chromosome an especially informative phylogenetic tree has previously been constructed from fully-sequenced chromosomes. This revealed contrasting bifurcating and starlike phylogenies for the major lineages associated with the Neolithic expansions in sub-Saharan Africa and Western Europe, respectively.

Results
We used coalescent simulations to investigate the range of demographic models most likely to produce the phylogenetic structures observed in Africa and Europe, assessing the starting and ending genetic effective population sizes, duration of the expansion, and time when expansion ended. The best-fitting models in Africa and Europe are very different. In Africa, the expansion took about 12 thousand years, ending very recently; it started from approximately 40 men and numbers expanded approximately 50-fold. In Europe, the expansion was much more rapid, taking only a few generations and occurring as soon as the major R1b lineage entered Europe; it started from just one to three men, whose numbers expanded more than a thousandfold.

Conclusions
Although highly simplified, the demographic model we have used captures key elements of the differences between the male Neolithic expansions in Africa and Europe, and is consistent with archaeological findings.

Modeling the contrasting Neolithic male lineage expansions in Europe and Africa (Sikora et al)

[cenkiss]

I think neandarthals were just another human community that got used to living in a colder climate. People are making wild assumptions about their supposed wildness and inhumane nature.

[G-Megas-Doux]

Regarding y-dna haplogroup R, as you said it originated outside of Europe and swept into Europe a couple thousand years before current era yet it is still dominant. About the time they swept into Europe would be equivalent of when the Celts are considered to have entered Europe. Before the rise of Greece the Celts are considered to have occupied much of Europe from Spain to Bulgaria and even some of the early Greeks may have been Celtic. There is a possibility that the later Germanic tribes were also part of the Celtic peoples originally as far as y-dna goes but the separation for such a long period allows for the linguistic changes, both are Indo European languages. At least that is my working theory that Celts and Germans had predominant y-dna of R and that is why it is dominant in Europe now.

Neanderthals were another human community descended from Homo Erectus however they are yet to find evidence of haplogroups transmitting to the current era from these people only autosome dna of around 4% in Caucasians are shared with known Neanderthal DNA. An example to be given is that it is known that Neanderthals had multiple hair colours as do modern humans however the red couloured hair of Neanderthals occurs due to a different mutation then in modern humans because the Neanderthals that are found to have bred with modern humans had dark hair mutations, so Europeans had to evolve red hair as a different mutation. So yes you can say that Home Sapiens did get used to living in a colder climate as there is also genetic evidence that light skin was evolutionally preferred due to the requirement of vitamin d from the sun as it is darker in less equatorial regions where darker skin is genetically preferred to limit burning.

Regarding Neanderthal nature, we cannot know what their nature was as not enough evidence has survived to the present to make a an informed accurate value judgement, all we can say is that they still had to achieve their basic needs like any other animal needed to stay alive. I count humans as animals in this stage of their evolution as they had much less technology to remove them from animalist lifestyles.

[Phier]

Where do the Sami fit in all this? They appear to be as far apart distance wise as the Arabs are to the rest of modern Europeans or for that matter neo and mesolithic Europeans.

[sumskilz]

I think neandarthals were just another human community that got used to living in a colder climate. People are making wild assumptions about their supposed wildness and inhumane nature.

Perhaps people wouldn't jump to those conclusions if they dressed a little better:

Neanderthals were another human community descended from Homo Erectus however they are yet to find evidence of haplogroups transmitting to the current era from these people only autosome dna of around 4% in Caucasians are shared with known Neanderthal DNA. An example to be given is that it is known that Neanderthals had multiple hair colours as do modern humans however the red couloured hair of Neanderthals occurs due to a different mutation then in modern humans because the Neanderthals that are found to have bred with modern humans had dark hair mutations, so Europeans had to evolve red hair as a different mutation. So yes you can say that Home Sapiens did get used to living in a colder climate as there is also genetic evidence that light skin was evolutionally preferred due to the requirement of vitamin d from the sun as it is darker in less equatorial regions where darker skin is genetically preferred to limit burning.

Although latitude alone wasn't enough to select for light skin it seems, it was also a matter of culture - specifically diet. European hunter-gatherers had dark skin. It was the farmers from the Middle-east who brought the alleles that were under stronger selection pressures as they moved north. There is also a possibility that sexual selection played a role. DNA evidence also suggests that ancient Fertile Crescent populations were somewhat fairer-skinned than typical modern populations in the region (this is still the case with genetically isolated populations). Northern Europeans, who have significantly more DNA from the dark-skinned Mesolithic hunter-gatherers than Southern Europeans do, are nevertheless fairer-skinned than Southern Europeans on average. Many things are different than has been previously assumed. This showcases at least two important point in my opinion:

1) Cultural practices can have a significant genetic effect in a relatively short period of time.

2) Specific alleles can be under strong selection pressures independent of general selection trends in the population.

This second point is also relevant two archaic DNA in modern humans. For example, most Neanderthal DNA was apparently under strong negative selection, while a few alleles were certainly under strong positive selection.

Where do the Sami fit in all this? They appear to be as far apart distance wise as the Arabs are to the rest of modern Europeans or for that matter neo and mesolithic Europeans.

Most likely they are the most recent arrivals in the region, or more accurately, they carry a genetic component from the people who brought their language to the region, and that genetic component is so different from the locals that it really pulls them away from the other clusters.

This is really relevant to the broader theme of the thread, but also helps situate the Saami:

Spoiler Alert, click show to read: 

MHG = [European] Mesolithic hunter-gatherers
NEOL = Neolithic farmers
West Eurasian UP = Upper Paleolithic West Eurasians
Solid lines = descent without admixture events
Dashed lines = descent through admixture events
Blue = living populations
MA1 = Mal’ta-1 (an Upper Paleolithic Siberian DNA sample)
K14 = Kostenki-14 (an Upper Paleolithic European from Russia)
Yenisei are the modern Siberian people who live Yenisei basin.

Source: Genomic structure in Europeans dating back at least 36,200 years (Seguin-Orlando, Korneliussen, Sikora, et al.)

It had been assumed by some that the Saami represent the pre-Indo-European population of the region, but then this haplogroup study found a discontinuity between the modern (including Saami) population and the Neolithic population. The closest living descendants are actually on the eastern coast of the Baltic. According to this PhD dissertation, which I can neither read nor have the expertise to really assess, “Proto-Germanic, Proto-Scandinavian, Proto-Finnic and Proto-Sami all date to different periods of the Iron Age… the pre-form of the Finnic and Samic languages – was spoken in the region of the present-day Finland in the Bronze Age, but not earlier than that…. [and] archaic (Northwest-)Indo-European language and a subsequently extinct Paleo-European language were likely spoken in what is now called Finland and Estonia, when the linguistic ancestors of the Finns and the Sami arrived in the eastern and northern Baltic Sea region from the Volga-Kama region probably at the beginning of the Bronze Age.”

Back to what I know better though, in 2010 a genome-wide study of the Saami was published that basically demonstrated that they are Russian-like, except with East-Asian and Native-American-like admixture. Why they didn't think to include Siberian samples in their study is beyond me. Guess what population is similar to both East Asians and Native-Americans?

So looking back at that phylogeny I posted, if you drew a dotted line from where West Eurasian and East Eurasian meet (that subsequently leads to Yenisei) and connect it to a dotted line from MHG, that is how the Saami fit in.

Here is a plot that adds more populations, which makes things both more confusing and more informative if you look at it long enough:

Spoiler Alert, click show to read: 

Source

[Phier]

Some of the Saami must be disappointed, everyone wants to be "first" into Europe, its like a internet thread.

[Ludicus]

On a side note, interesting news,
First human' discovered in Ethiopia

Prof Chris Stringer of the Natural History Museum in London described the discovery as a "big story".
He says the new species clearly does show the earliest step toward human characteristics, but suggests that half a jawbone is not enough to tell just how human it was and does not provide enough evidence to suggest that it was this line that led to us.

Sumskilz, I would like to hear your opinion.

[sumskilz]

On a side note, interesting news,
First human' discovered in Ethiopia


Sumskilz, I would like to hear your opinion.

I agree with the Stringer quote, but you really can't fault Villmoare for making the argument that it's transitional to the Homo genus, because it is possible and the headlines which come from such an argument are probably going to bring more money in for his research, which is good either way.

Here's a closer look:

Spoiler Alert, click show to read: 

Back to the topic, which I left some what incomplete, there was a third major migration into Europe but until recently, there has been a lot of uncertainty about the extent to which it left a genetic impact. This paper was only officially published yesterday, but it was actually the inspiration for me starting this thread since they had quietly distributed a preprint:

Massive migration from the steppe was a source for Indo-European languages in Europe (Haak, Lazaridis et al.)

Abstract: We generated genome-wide data from 69 Europeans who lived between 8,000–3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000–5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000–7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000-year-old Siberian. By ~6,000–5,000 years ago, farmers throughout much of Europe had more hunter-gatherer ancestry than their predecessors, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~75% of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for a steppe origin of at least some of the Indo-European languages of Europe.

Here is a plot of the ancient individuals used in the study showing their relationship to each other:

Spoiler Alert, click show to read: 

The gray points represent modern populations. To understand who they are, you'll have to look at previous plots I've posted.

Here are the admixture proportions of the three major ancient populations in modern populations and ancient individuals:

Spoiler Alert, click show to read: 

[6644kp]

So it looks like modern Europeans are overwhelmingly part Middle Eastern farmer and part Aryan steppe invader. The European hunter-gathered got crushed, except for the Estonians they don't seem to have much ME farmer in them.

[sumskilz]

So it looks like modern Europeans are overwhelmingly part Middle Eastern farmer and part Aryan steppe invader. The European hunter-gathered got crushed, except for the Estonians they don't seem to have much ME farmer in them.

Yeah, the people from the steppe, the Yamnaya culture in archaeological terms, were themselves a composite population - descended from a mix of about half Eastern European hunter gatherers and half Middle Eastern Farmers who had come up through the Caucasus. The most likely scenario is the proto-Indo-European speaking Eastern European hunter gatherers domesticated the horse and invented the chariot, then conquered and assimilated the Middle-Eastern farmers who had moved north of the Caucasus.

Until enough ancient DNA samples were gathered, this was hard to sort out because the Middle Eastern farmers who came through the Caucasus were of course cousins of those who had come through the Mediterranean into Europe previously. The first wave of Middle Eastern farmers were very similar to modern isolated Levantine populations like Samaritans, while the Middle Eastern farmers assimilated into the Yamnaya culture were very similar to modern Armenians – basically Western and Northern branches (respectively) of Fertile Crescent populations, prior to the demographic changes brought on by later conquests.

All of this supports the Kurgan Hypothesis for the spread of the Indo-European languages:



David W. Anthony wrote a book on this called The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World, but seems to believe it was mostly by means of cultural assimilation and hegemony, the type of explanation that's been more en vogue that last 50-60 years, whereas prior to that everyone was imagining conquests as extermination and replacement. Genetic evidence, especially from ancient samples, is more solid and the story it tells is somewhere between the two models. Based on haplogroups, the conquering male lineages became predominate either by just having more children as a ruling class or because the conquered men were killed off (probably a bit of both).

What's weird to me, is that the original hunter gatherer maternal lineages almost disappeared when the first Middle Eastern farmers showed up. That means that the hunter gather population was very low and just out competed, or it could mean the conquering/migrating males weren't very interested in the local women, maybe even killed them off with the men. In contrast, when the steppe people conquered the farmers, that was not the case.

[6644kp]

Yeah, the people from the steppe, the Yamnaya culture in archaeological terms, were themselves a composite population - descended from a mix of about half Eastern European hunter gatherers and half Middle Eastern Farmers who had come up through the Caucasus. The most likely scenario is the proto-Indo-European speaking Eastern European hunter gatherers domesticated the horse and invented the chariot, then conquered and assimilated the Middle-Eastern farmers who had moved north of the Caucasus.

Until enough ancient DNA samples were gathered, this was hard to sort out because the Middle Eastern farmers who came through the Caucasus were of course cousins of those who had come through the Mediterranean into Europe previously. The first wave of Middle Eastern farmers were very similar to modern isolated Levantine populations like Samaritans, while the Middle Eastern farmers assimilated into the Yamnaya culture were very similar to modern Armenians – basically Western and Northern branches (respectively) of Fertile Crescent populations, prior to the demographic changes brought on by later conquests.

All of this supports the Kurgan Hypothesis for the spread of the Indo-European languages:



David W. Anthony wrote a book on this called The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World, but seems to believe it was mostly by means of cultural assimilation and hegemony, the type of explanation that's been more en vogue that last 50-60 years, whereas prior to that everyone was imagining conquests as extermination and replacement. Genetic evidence, especially from ancient samples, is more solid and the story it tells is somewhere between the two models. Based on haplogroups, the conquering male lineages became predominate either by just having more children as a ruling class or because the conquered men were killed off (probably a bit of both).

What's weird to me, is that the original hunter gatherer maternal lineages almost disappeared when the first Middle Eastern farmers showed up. That means that the hunter gather population was very low and just out competed, or it could mean the conquering/migrating males weren't very interested in the local women, maybe even killed them off with the men. In contrast, when the steppe people conquered the farmers, that was not the case.

I'm sure you read some of the new discoveries that said that the ancient (8000YBP) European hunter gatherers were dark skinned but surely this could not have been the case since large scale intermixing happened with the light skinned ME farmers. Would not this not mean that modern European populations would need to look mixed? Especially the Estonians for example? Why aren't there many brown Europeans? I we look at modern Middle Eastern populations the introduction of even small amounts of African and Indian genetics through the Arab slave trade "brownified" and made them have more off Caucasian facial features.

Maybe the European hunter gatherers were darker than the farmers but it could not have been by much they would have to had a Mediterranean appearance at least for Modern Europeans to become in terms of skin color so homogenous.

[sumskilz]

Before I get into this pigmentation stuff, I should mention that the blue eye allele came from the darker skinned hunter gatherers.

I'm sure you read some of the new discoveries that said that the ancient (8000YBP) European hunter gatherers were dark skinned but surely this could not have been the case since large scale intermixing happened with the light skinned ME farmers. Would not this not mean that modern European populations would need to look mixed? Especially the Estonians for example? Why aren't there many brown Europeans? I we look at modern Middle Eastern populations the introduction of even small amounts of African and Indian genetics through the Arab slave trade "brownified" and made them have more off Caucasian facial features.

Maybe the European hunter gatherers were darker than the farmers but it could not have been by much they would have to had a Mediterranean appearance at least for Modern Europeans to become in terms of skin color so homogenous.

The simple answer to this is that people eating a farmed diet were under significant positive selection for light skin independent of other features including facial features. The degree of selection would have been much stronger in Northern Europe than in Southern Europe or the Mediterranean, so the change wasn't only a matter of admixture, but selection. Admixture alone would have just resulted in people being halfway between, but Estonians are as light as anyone in Northern Europe. So despite having very light skin, Estonians probably do look a bit like the hunter gatherers did structurally, at least more so than other modern Europeans do.

Here is reconstruction based on both the skull and the DNA (usually they only use the skull):




Their skulls don't look like typical modern European skulls to me, this one is pretty typical for them. Although they do look more like modern Europeans than anyone else I would say, and probably by chance combination there are some modern Europeans who look more or less similar but with lighter skin.

Here's another skull from a completely different site, but you can see the morphological similarities:



This guy also had blue eyes.

EDIT: In contrast, these are Neolithic farmers whose ancestors came entirely from the Middle East (the skull in the second pic looks young, maybe female):





Next are Sixteenth Century Capuchin monks for comparison, probably from various European Catholic countries (maybe mostly Italians):



For anyone interested, I can go into more detail about the pigmentation...

These are the three alleles most responsible for European pigmentation, but there are a few others that have a lesser effect.

SLC24A5:

SLC24A5 accounts for about 40% of the pigmentation difference between Europeans and sub-Saharan Africans. The frequency of the light skinned variant in modern Europeans is 99.6%. If a person has one light version and one dark version, they will be halfway in between. It is also the main reason Middle-Eastern people are lighter than sub-Saharan Africans. East Asians are lighter because of a different gene. This is it's modern distribution, the light skinned version is in blue:

Spoiler Alert, click show to read: 

No Mesolithic European hunter gathers tested have had the light skinned version. Almost all of the Neolithic Middle Eastern farmers tested had two copies of the light version.

If you only looked at the SLC24A5 though, you'd think a lot of North Africans are as light as Northern Europeans which is clearly not the case even when the effects of sun exposure are taken into account, but there are other genes...

SLC45A2:

SLC45A2 is another gene that is responsible for a significant amount of European's pigmentation. It's frequency is 97% in modern Europeans. This is it's modern distribution:

Spoiler Alert, click show to read: 

Yellow is the light version. You can see some modern Italians, for example, only have one copy of the light versions. Most modern Middle Easterners have two of the dark version or one light and one dark. The light version of this gene also contributes to the pinkish tint of European skin.

No Mesolithic European hunter gatherers have been found to have the light version. However neither did most Neolithic Middle Eastern farmers. Only a minority of them had a single copy of the light version. This one was apparently not significantly selected for in the Middle Eastern environment, but very much so in Europe.

TYRP1:

TYRP1 affected both skin and hair color. The light version appears at a frequency of 59.9% in modern Europeans, was not present in Mesolithic European hunter gatherers, and appeared at a frequency of 41.6% in Neolithic Middle Eastern farmers.

Evidence of positive selection...

The Mesolithic European hunter gatherers didn't have any of the alleles for the light versions of these genes, but even though the Neolithic Middle Eastern farmers were the source of the light alleles, they didn't occur at as high of a frequency in them as they do in modern Europeans. Here are the frequencies of the light versions together:

SLC24A5 Modern Europe: 99.6%
SLC24A5 AME farmers: 90%

SLC45A2 Modern Europe: 97%
SLC45A2 AME farmers: 12.5%

TYRP1 Modern Europe: 59.9%
TYRP1 AME farmers: 41.6%

The estimates are a little rougher for the ancient DNA because of small sample size, but the basic pattern is still clear. The farmers skin got lighter because of their diet, but they needed to be even lighter once they entered Europe. The assimilated darker alleles from the hunter gatherers were selected against because they were eating a farmed diet. Sexual selection may also have played a role.

Here's a good study on the topic: Genome flux and stasis in a five millennium transect of European prehistory

[6644kp]

That is quite fascinating, one could imagine a person like the first digital reconstruction that you showed to be the norm in prehistoric Europe. He is definitely darker than Modern Northern Europeans yet not so dark too cause a mixed looking population to occur. That the relatively low percentage of ancient hunter gatherer DNA left in modern Europeans and sexual selection at the time for females with ever lighter skin can indeed give a detailed picture of why Europe is not just white but why Northern Europe is so especially fair skinned.

[Phier]

EDIT: In contrast, these are Neolithic farmers whose ancestors came entirely from the Middle East (the skull in the second pic looks young, maybe female):

Can't tell sex, but most likely age of death between 8-10.

[sumskilz]

Can't tell sex, but most likely age of death between 8-10.

I figured you'd be good at that. I was thinking 10-12 initially, but your assessment makes more sense. I thought the squarish eye orbits and maybe U rather than V shaped mandible suggested male, can't see where the zygomatic arch ends, but the complete lack of any brow ridge made me think female. Though in light of your age estimate, all that seems less relevant. Are you going mostly by the shape or is there also something about the teeth (other than the lack of wear)?

Check out this guy from Upper Paleolithic Russia:



Seems like a lot of testosterone there. He has less than 2% Neanderthal admixture, but it's in larger segments than modern Eurasians, so it wasn't that far back for his family.

EDIT: Also may be from a phylogenetic dead-end, population-wise

[Phier]

I figured you'd be good at that. I was thinking 10-12 initially, but your assessment makes more sense. I thought the squarish eye orbits and maybe U rather than V shaped mandible suggested male, can't see where the zygomatic arch ends, but the complete lack of any brow ridge made me think female. Though in light of your age estimate, all that seems less relevant. Are you going mostly by the shape or is there also something about the teeth (other than the lack of wear)?

I found this hi res picture..
http://upload.wikimedia.org/wikipedi...erxheim_01.jpg

The second molars are just starting to erupt.
The first and second primary molars are mostly intact AND the roots are still clearly visible on the first (instead of resorpted)
It appears the primary canines were lost after death and were also fully rooted or close to it.

If anything the skull might be closer to 8 then 10, but there is a LOT of variation, I fudged a bit, assuming a "primitive" population might mature slightly faster.

I'm personally leaning towards female slightly.

Jaw - Looks a bit more male, but young so still growing.
More rounded eye socket - female
Superior of eye orbit - female
Can't really see the zygomatic arch termination -either
Ramus - more male
Brow ridge - female

The only reason I'm leaning female is the jaw seems to have more variation in populations, but thats just an educated guess. The age does throw me off a bit, I have only limited experience dealing with children's skulls, so I'm not sure when some of these variations in skull morphology happen.

[sumskilz]

I found this hi res picture..
http://upload.wikimedia.org/wikipedi...erxheim_01.jpg

The second molars are just starting to erupt.
The first and second primary molars are mostly intact AND the roots are still clearly visible on the first (instead of resorpted)
It appears the primary canines were lost after death and were also fully rooted or close to it.

If anything the skull might be closer to 8 then 10, but there is a LOT of variation, I fudged a bit, assuming a "primitive" population might mature slightly faster.

I'm personally leaning towards female slightly.

Jaw - Looks a bit more male, but young so still growing.
More rounded eye socket - female
Superior of eye orbit - female
Can't really see the zygomatic arch termination -either
Ramus - more male
Brow ridge - female

The only reason I'm leaning female is the jaw seems to have more variation in populations, but thats just an educated guess. The age does throw me off a bit, I have only limited experience dealing with children's skulls, so I'm not sure when some of these variations in skull morphology happen.

Thanks, this is something I'd like to get better at, but haven't really put in the time since it's kind of redundant for the work I've been doing lately since there are always specialists who do everything for the reports. Those guys can sort of be dicks about the DNA analysis though, many I've encountered anyway. If they get remains in their labs, they don't want anyone coming near them, even to take a DNA sample (or maybe especially to take a DNA sample) until they've finished doing everything they want to do. I noticed in that National Geographic documentary Quest for the Phoenicians, Spencer Wells runs into that same attitude.

A new study published a couple days ago relevant to the thread:

A recent bottleneck of Y chromosome diversity coincides with a global change in culture

Abstract: It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

These coincide with the Upper Paleolithic Revolution and the Agricultural Revolution. The first one is small because it is the male lineages of the Out-of-Africa population who were a relatively small population who developed behavioral modernity and subsequently colonized the rest of the world. The second bottleneck is really pronounced and doesn't occur at all in the female lineages. The Middle Eastern farmers who largely replaced the hunter gatherers in Europe fit this pattern. As does the invasion from the steppe which was half descended from an agricultural population, and in any case had some technological advantages, who largely displaced the male lineages in many parts of Europe even where they incorporated much of the previous wave's population.

Dienekes Pontikos made an interesting observation about this study on his blog:

Most human mythologies contain stories of "first men" and eponymous founders of nations; these were often ridiculed in recent times as invented stories whose purpose was to engender social cohesion through a story of shared descent. But, now it seems that these stories were at least in part true, and such ultra-prolific patriarchs do indeed stand at the beginning of many later lines of descent.

[Phier]

Thanks, this is something I'd like to get better at, but haven't really put in the time since it's kind of redundant for the work I've been doing lately since there are always specialists who do everything for the reports.

Yea, and I wouldn't trust them 100% either. I was recently looking at a 30k year old cro magnon skeleton and noted the age to be about 18. A curator was there and said "some have said that, but our experts blah blah blah 30's due to the wear on the bones."

*sigh*

So this young woman lived a VERY hard life and died young, but you can't fake teeth (which didn't have that much wear on them for the time period). Teeth are one of the most conserved structures in the human line, with the same patterns long before Lucy. I could be wrong by a few years, especially since they may have had some different ages for eruption, but if anything they would have erupted earlier. You don't need teeth coming in, in your 40's.

Was good though, I was able to see all the xrays they had etc, I think I convinced the curator at least

A recent bottleneck of Y chromosome diversity coincides with a global change in culture

I have never seen so many authors on a paper before.

These coincide with the Upper Paleolithic Revolution and the Agricultural Revolution. The first one is small because it is the male lineages of the Out-of-Africa population who were a relatively small population who developed behavioral modernity and subsequently colonized the rest of the world. The second bottleneck is really pronounced and doesn't occur at all in the female lineages. The Middle Eastern farmers who largely replaced the hunter gatherers in Europe fit this pattern. As does the invasion from the steppe which was half descended from an agricultural population, and in any case had some technological advantages, who largely displaced the male lineages in many parts of Europe even where they incorporated much of the previous wave's population.

A couple of years ago I was reading something about the genetics of the UK, and there was an apparent Y chromosome extinction (but not Mt) which the author missed the implications of. I wish I would have saved that link. It doesn't take a lot of imagination to figure out why this sort of thing happens.