December 26, 2013

Ancient DNA: what 2013 has brought

I was looking at my ancient DNA tag for the last year and it seems we've learned quite a lot in 2013. Here's my short summary of some major studies, news articles and reports:
  • 400,000 year old Homo heidelbergensis in Iberia had mtDNA similar to Middle Paleolithic Denisovans from the Altai. This is important because of the age of the sample which opens up new vistas for ancient DNA research and because it is the first  link to the mysterious Denisovans.
  • A Neandertal inhabited the same cave where the Denisovan fingerbone was found. Denisovans had Neandertal admixture as well as admixture with an unknown "ultra-archaic" group; Eurasians have admixture from a Neandertal most similar to the Mezmaiskaya sample from the Caucasus; East Eurasians have a little bit of Denisovan admixture, while Australasians have a lot more; and all Sub-Saharan Africans seem to have a little bit of Neandertal admixture too, via West Eurasians during the Holocene.
  • A ~24,000 year old Upper Paleolithic Siberian from Mal'ta is related to Native Americans who are a mix of it and East Asians. Mal'ta was related to West Eurasians and not to East Eurasians. It belonged to Y-haplogroup R* and mt-haplogroup U*.
  • On the other hand, a ~40,000 year old from China was definitely East Eurasian.
  • Europeans are a 3-way mix of Neolithic farmers, Mesolithic hunter-gatherers and aforementioned UP Siberian-like "Ancient North Eurasians"; Early LBK farmers from Central Europe resemble later Oetzi, Swedish farmers, and probably Iberian farmers too. They also had mysterious "Basal Eurasian" ancestry from the deepest split of the Eurasian tree. Mesolithic Europeans had lots of Y-haplogroup I.
  • Ancient mtDNA reveals that something happened during the late Neolithic and early Bronze Age in Germany; the populations from that time are the first ones who appear quasi-modern in their haplogroup frequencies. It also turns out that hunter-gatherers didn't disappear in Germany after the LBK came along. And mtDNA haplogroup H, most frequent in modern Europeans, established itself around the Mid-to-Late Neolithic.
  • West Siberia had a West/East Eurasian admixed population during the Bronze Age, like earlier ages.
  • Lots of hints of interesting events in the European steppe too.
  • Modern Tuscans probably not descended from ancient Etruscans; discontinuity seems to be the rule.
  • Minoans were fairly regular Europeans, not North African (they had little mtDNA U, though, maybe like Mesolithic Greeks).
  • A lot more mtDNA haplogroup U from really old Europeans, and mtDNA haplogroups M+N date to ~77 thousand years ago.
  • Mesolithic west Europeans had blue eyes, but Neolithic Europeans had brown ones and European steppe populations "darker" than modern Europeans). ~8,000 year old Europeans had dark brown or black hair (at least two of them).
I bet 2014 will be equally exciting!

45 comments:

Davidski said...

Have you been able to download that new Human Origins dataset? Apparently it should be here, but it never works for me.

http://genetics.med.harvard.edu/reichlab/Reich_Lab/Datasets.html

Ken said...

It is most unlikely Mesolithic west Europeans had blue eyes, but darker skin than the LBK. There would be no reason for it in hunters, if vitamin D was supplied from meat and fish, and light eyes were a side effect of lighter skin for increased synthesis of vitamin D needed bu agricultural populations. No population has light eyes and dark skin today. Not a one. We know Mesolithic hunters had blue eyes, it is reasonable to assume they had light skin, and hair.

European steppe populations "darker" than modern Europeans should be no surprise. Who thought that hair and eye colours came from Indo Europeans?

"~8,000 year old Europeans had dark brown or black hair at least two of them."

Lots still do.

Fanty said...

@Ken:

Well, yeah theoretically skin/hair/eye migmentation should be related.

On the other hand, its said, unlike with skin pigmentation, eye pigmentation has no positive or negative effect. And the scientists who, years ago, researched the genetics behind blue eyes said, the only reason, why blue eyes could become so widespread is because humans enforced it (Breeded children with blue eyes (possibly killed others?) in kind of religious fetish or something.

They even used the term "Hunter gatherer tribes" at that time, as if they already knew, from who these originated.

Ah and here are some examples of people who are not perfectly white but have blue eyes (of course, most of them are mutts, sometimes they may just "tanned" by the sun or solar studio :-D :

http://25.media.tumblr.com/tumblr_m8bezeDlqA1qjfghyo1_500.jpg

http://s3.hubimg.com/u/6487178_f520.jpg

the extreme case:
http://bestuff.com/images/images_of_stuff/210x600/people-with-dark-skin-and-light-eyes-202619.jpg

http://3.bp.blogspot.com/_vvAhyR-6PAM/TJlv_8g4ILI/AAAAAAAAGA8/mfYLhr_xI34/s1600/blue-eyedAfghan.jpg

http://1.bp.blogspot.com/_vvAhyR-6PAM/TJlwAaXYBMI/AAAAAAAAGBE/5zHUhwOOUbU/s1600/img_9753b.jpg

terryt said...

"I bet 2014 will be equally exciting!"

I'm sure of it.

"A ~24,000 year old Upper Paleolithic Siberian from Mal'ta is related to Native Americans who are a mix of it and East Asians. Mal'ta was related to West Eurasians and not to East Eurasians".

Believe it or not, many commenters at this blog still refuse to accept that statement. You know who they are of course.

"Europeans are a 3-way mix of Neolithic farmers, Mesolithic hunter-gatherers and aforementioned UP Siberian-like 'Ancient North Eurasians'"

Nor are the same people prepared to accept any connection between Mesolithic hunter-gatherers and aforementioned UP Siberian-like Mal'ta individual. Amazing, isn't it?

"No population has light eyes and dark skin today".

Not entirely true. Many New Zealand Maori with some European ancestry have blue eyes and darker skin than Europeans.

Tobus said...

Of the 3 major "European" light skin SNP's (SLC24A5, SLC45A2 and TYR) Loschbour has the ancestral dark-skin variant at all 3, Stuttgart has 1 dark, one light and 1 heterozygous, and Otzi has 2 light. If this is representative it seems that "white" skin is very recent indeed... at least in Europe.

bmdriver said...

"~8,000 year old Europeans had dark brown or black hair at least two of them."

Yes, as they are a migration from India and Indians.

barakobama said...

Tobus, where did you hear Loschbour has the ancestral dark skin variant in those three SNP's? I really doubt he and most Mesolithic Europeans had dark skin.

You cant generalize all ancient Europeans as the same people. The farmers and hunter gatherers are the two major ancestral populations to modern Europeans. They were not very related to each other besides being west Eurasian and some mixing between the two. So when debating when light skin developed in modern Europeans you have to remember that. Light skin would not have developed in both those populations at the same time.

So far 2/2 Mesolithic European samples have blue eyes. There is no way if they had a high amount of blue eyes that they also had dark skin, that doesn't exist today. When ever I tell people that, they cherry pick pictures off the internet of blue eyed Indians. But what dark skinned people have over 5% blue eyes? Probably none, and if there is one like maybe Kablye they are also known for other European features including light skin.

In Europe today generally the more Mesolithic ancestry(based in autosomal DNA) the more light hair and eyes a population has. That is why I am not surprised with 2/2 blue eyes from Mesolithic Europe so far.

I have heard some say well blue eyes came from the dark skinned Mesolithic people while light skin comes from the farmers. How does that make any sense? Dark haired and eyed European populations(have more farmer ancestry) also have darker skin and are known as olive, while very light haired and eyed Europeans have much lighter skin.

Since blue eyes are so popular in Baltics(highest amount of Mesolithic ancestry) then why don't they have dark skin? The saying has always gone light skin, blue eyes, and blonde hair not dark skin and blue eyes. If your guys theory's that Mesolithic Europeans had blue eyes and dark skin was correct then the saying wouldn't connect it with light skin. Even ancient Romans connected light eyes with light skin. There is no doubt the blue eyes found in Mesolithic Europe is connected with blue eyes in Europe today.

I think some people assume or have a tendency to think light features in Europe are recent, I know there is something psychological behind it.

mooreisbetter said...

The more things change, the more they stay the same.

The hardcore, real, genuine scientists have been saying these things for years, really. They just don't say it with the certainty and pop-sci packaging that certain people use.

Recall the seminal paper on the I-M170 Y chromosome line by Siri Rootsi in 2005-2006. In it, she posited that:

(1) Hg I was the second major line of AMHS in Europe. That it came it with the Gravettian wave of settlement, and has been there at least since the Mesolithic.

(2) That the first line in Europe, contrary to certain modern speculation (that it was C, or even A00), was likely R* or R1*.

(3) That an explosion of colonization from pockets of I located primarily in the Balkans but also perhaps Italy or Spain -- intro central Europe and up into Scandinavia -- is the reason for the R1a and R1b split we see today.

And lo and behold, this was all true.

Dienekes said...

(2) That the first line in Europe, contrary to certain modern speculation (that it was C, or even A00), was likely R* or R1*.

...

And lo and behold, this was all true.


In case I missed some episodes, what is the ancient DNA evidence that R* or R1* was the first line in Europe?

barakobama said...

The theory's that R1b and R1a lines in Europe have been there since the Mesolithic have actually been proven incorrect. R1b L11 arrived in west Europe just 5,000bp and took most of west Europe by 3,000bp probably spread by Indo Europeans Germans, Celts, and Italians. R1a1a1 M417 which takes up almost all modern R1a is descended from many different Indo European migrations out of far eastern Europe, during the copper-bronze age.

terryt said...

"I have heard some say well blue eyes came from the dark skinned Mesolithic people while light skin comes from the farmers. How does that make any sense?"

Exactly.

"I think some people assume or have a tendency to think light features in Europe are recent, I know there is something psychological behind it".

I think you are correct here too. If light skin is an environmentla adaptation it cannot have developed very recently. It must be fairly ancient.

Locrian said...

barajobama wrote : “R1b L11 arrived in west Europe just 5,000bp and took most of west Europe by 3,000bp probably spread by Indo Europeans Germans, Celts, and Italians. R1a1a1 M417 which takes up almost all modern R1a is descended from many different Indo European migrations out of far eastern Europe, during the copper-bronze age.”


What is the evidence for there being any R1b in Europe even in the Bronze Age? Where was the individual that supplied this?

The earliest R1b that I know of was from Tutankhamen — and thus presumably Akhenaten., and that was 1300 bc. Can you name any ancient remains in Europe that have shown R1b before this date?

mooreisbetter said...

@Dienekes: The theory that R* or R1* was the first in Europe stems from logic, a discipline that you Greeks invented.

We have the Ma'lta Siberian as R*, and it is one of the oldest Eurasian Ancient DNA samples -- period. There is our fact.

The Ma'lta sample would certainly be as close as the Ancient North Eurasian cohort in the second paper.

Of modern populations, those with the highest percentages of both R1b and R1a also bear the highest percentages of Ancient North Eurasian: Scots and Basques have equal percentages to Belorussians and other Eastern Europeans.

In other words, we have two facts:

(1) an Ancient North Eurasian sample was R*

(2) Modern R-descended populations are the most "Ancient North Eurasian."

leading us to this conclusion.

Face it: R1 lines are a European mirror for Ancient North Eurasian. Which makes sense, because we have clear evidence that the R lines are Ancient, north, and Eurasian.

mooreisbetter said...

@barakobama.

Give it a rest, will you?

By the time that most identifiable ethnic groups existed, even IEs or PIEs, people were already a mosaic of Y-lines.

I could buy that R1b expanded with a population explosion of milk-digesters, outcompeting the lactose intolerant during an epoch of grave famine. Those milk digesters even likely worshipped their new abilities so much, they buried their dead with udder-like drinking cups (bell beakers).

But your notions of R1b expanding with a group of langauge speakers is laughable.

Model things backward:

Modern Spaniards are a mix of peoples. They probably have 20+ Y chromosome lines.

2000 years ago, Spaniards were a little less admixed, mostly Celtiberians and Tartessians and Romans: They probably had 15+ Y chromosome lines.

2000 years before that, they were a little less admixed. Still 10+ lines.

You have to go back to the dawn of time to make broad statements like yours accurate.

Tobus said...

@barakobama:
Tobus, where did you hear Loschbour has the ancestral dark skin variant in those three SNP's? I really doubt he and most Mesolithic Europeans had dark skin.

It's in the supplementary info table S7.1 (p. 37) - rs16891982 (both have dark), rs1426654 (Losch dark, Stutt light) and rs1042602 (Losch dark, Stutt hetero). One of the many studies associating these alleles with light skin can be found here.

Two recent studies have suggested the selective sweeps for the light alleles occurred at least 10kya, so I too find these results surprising. If they hold up it would seem that "white" skin may evolved outside Europe and migrated in later. I should note that Razib has already hypothesised this for SLC24A5 which is found all through West and South Asia, but the other two are mostly restricted to Europe.

So far 2/2 Mesolithic European samples have blue eyes. There is no way if they had a high amount of blue eyes that they also had dark skin, that doesn't exist today.

Loschbour only has a 50% probability of having blue eyes - he just as likely didn't as he did... given the 100% probability that he didn't have modern European skin colour, the logical assumption would be that he didn't have blue eyes, not that he didn't have dark skin. The published La Brana DNA coverage doesn't include any of the skin colour alleles (neither do the Swedish samples unfortunately), so he may well have had light skin to match his blue eyes - we just don't know.

AFAIK blue eyes and light skin evolved independently, with light skin being an adaptation to UV, but blue eyes being driven primarily by sexual selection. If that is the case then it's certainly *possible* that ancient populations had a mix of the two, even if such a phenotype no longer exists today.

Dark haired and eyed European populations(have more farmer ancestry) also have darker skin and are known as olive, while very light haired and eyed Europeans have much lighter skin.

This is a common fallacy, what you are seeing is increased tanning response. Empirical studies using non-exposed areas of skin (inside upper arm generally) show no difference in skin reflectance between Mediterraneans and Northern Europeans (see Table 6 in Jablonski 2000).

I think some people assume or have a tendency to think light features in Europe are recent, I know there is something psychological behind it.

The original assumption was that Cro-Magnon was white and represented the ancestors of modern Europeans. In the last 10 years scientists have found evidence of multiple migrations and replacements into Europe and have discovered the genetics behind depigmentation are less than 20kya old, meaning Cro-Magnon was probably dark-skinned and not a direct ancestor of modern Europeans. As more ancient DNA comes to light we get a better picture of when and where light skin developed, and these latest mesolithic finds suggest it wasn't widespread in Europe 8,000 years ago. Contrary to what you "know", it's science that suggests "white" skin is a recent phenomenon, at odds with the "psychological" assumption that Europeans have always had same phenotype that they do today.

Dr Rob said...

"Mesolithic Europeans had lots of Y-haplogroup I."

Which specific papers show that, Dienekes ? Thanks

eurologist said...

Tobus,

I have not read too many papers about that, but my intuition (and anecdotal experience) tell me that some genes resulting in dark skin are independent of light exposure, but others very much are.

It is an incredible benefit to have seasonally adjusting skin UV filtering, given that both vitamin D production and protection against folic acid loss must be optimized.

As a result, some people get much darker and much more easily so under the influence of UV exposure.

Simon_W said...

@ Locrian

See here:
http://dienekes.blogspot.ch/2012/05/bell-beakers-from-germany-y-haplogroup.html

Simon_W said...


Mooreisbetter, I'm buying your two facts, but don't see how this proves that R1 was the first lineage in Europe. In particular it doesn't follow that R1 was present in western Europe since the paleolithic. In fact, the recent finding that both the Western European hunter-gatherers, as well as their Scandinavian fellows were considerably less ANE admixed than many modern Europeans clearly contradicts with such a conclusion.

As for your objection to theories linking the spread of haplogroups to the spread of ethnic groups – I cannot agree fully. I think these theories work with simplifications – they speak of „the haplogroup“ of an ethnic groups as if it just had one – but I think by this they actually just mean the predominant one or two haplogroups. And there are examples where haplogroups spread with the migration of an ethnic group. For instance, who introduced R1b to Mexico? The Spaniards. Even though they had plenty of other haplogroups.

Eastern View said...

I wonder why the most important implication keeps getting ignored.

Supplement 10 of Lazaridis also makes it probable that Near Eastern populations are over 60% Basal Eurasian while Baltic Europeans are over 85% Derived Eurasian.

This makes two poles of 2 totally different races, one basal, the other more related to non-Near Eastern Eurasians.

Dienekes said...

Which specific papers show that, Dienekes ? Thanks

The paper I link to in that bullet point.

matt said...


The report that 19 of 3700 men had the same ydna ancestors as Otzi gives one data point on current ydna probability versus 5000 years ago.

http://www.bbc.co.uk/news/world-europe-24477038

Ken said...

"It is an incredible benefit to have seasonally adjusting skin UV filtering, given that both vitamin D production and protection against folic acid loss must be optimized"

1)If the sun or ultra violet light really destroyed appreciable amounts of folic acid there would be rather noticeable consequences from sunbathing and sunbed use. You see an epidemic of pernicious anemia and birth defects in sun worshipers?

3)The origin of European skin lightening is too late for straight vitamin d at latitude to be the answer. Modern humans lived in north Europe during the Upper Pleistocene without light skin, as the de-pigmentation in Europe is dated at between 19,000 and 11,000 years ago.

3) White skin is dated before blue eyes and the mechanisms of sex recognition mean light skin would need to be there before blue eyes. See here.

4)Farming having reduced dietary vitamin D sources, was supposed to have led to selection for lighter skin and maximizing of vitamin D synthesis for resistance to rickets, cancer and infectious diseases, in high latitudes. The evolution of light eye and hair coloration was still supposed to be a side effect of natural selection for vitamin D, but in farmers.

The relevance of blue eyes being around in the European Mesolithic (ie pre-agriculture) is that is too long ago for an agriculture hypothesis. The only explanation for blue eyes that still makes sense is sexual selection.

Locrian said...

Simon_W : thanks for the link. I’d forgotten that find. 3000 bc in Germany is certainly interesting. It would be nice to find it in Spain around the same time or earlier however to consolidate its association with Bell Beaker.

On the presence of R1b in the 18th Dynasty of Egypt, I think it is a great shame that the largest repository of ancient dna is not being examined and it’s links to the rest of the region studied. Egypt has become the elephant in the room when ancient populations are discussed: the most powerful culture anywhere close to Europe for 2,000 years and it is treated as though it is not there, either as a source of populations or sink. It’s the kind of blindness that can’t last.

Tobus said...

@Eurologist: As a result, some people get much darker and much more easily so under the influence of UV exposure.

This "environmental" darkening (ie tanning) is deliberately excluded when searching for cross-populatiation pigmentation genes by using unexposed skin when measuring skin "colour". From my understanding the ability to tan is the ancestral state and is common to all populations. It's only in low UV areas like northern Europe that the non-tanning (sunburn!) phenotype reaches any kind of significance, likely due to relaxed conditions as opposed to positive selection.... many southern European populations have retained the tanning ability while still being just as depigmented as in the north.

@Ken: If the sun or ultra violet light really destroyed appreciable amounts of folic acid there would be rather noticeable consequences from sunbathing and sunbed use

Any such problems in the modern era would be covered up by improved diet and medical treatment. One alternate theory is that the increased melanin provides an epidermal barrier to infection. Whatever the reason, it does seem that dark skin has been under extremely high functional constraint in the tropics and high-UV areas for hundreds of thousands of years. It could be argued that light skin results from a relaxation of this constraint combined with sexual selection as opposed to being a better low-UV phenotype in itself, especially given the existing sexual dimorphism in this regard in all populations.

eurologist said...

"If the sun or ultra violet light really destroyed appreciable amounts of folic acid there would be rather noticeable consequences from sunbathing and sunbed use. You see an epidemic of pernicious anemia and birth defects in sun worshipers?"

Ken,
I don't understand your logic. That is exactly the reason why seasonally adjustable skin color developed. Also, the Vitamin D / folic acid balance is not my theory.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3795437/
http://www.hormones.gr/703/article/article.html

Ken said...

Eurologist, I'm afaid your first ref which confidently asserts ("damage by UV for folic acid generation [sic])ref is in conflict with the second which says "direct photodegradation of folates may not be the mechanism of biological significance."

Although 'IN aqueous solutions, in blood and even in human skin, folic acid may be degraded by ultraviolet radiation', our ancestors they did not have 'Folic acid' in the blood (ie 'unmetabolized folic acid in serum', which is problematic for genome stability and overall health. See here. The form of folate that humans naturally have after ingesting food (as opposed to supplements) is methyltetrahydrofolate. Not only is it probably better for maintaining genomic stability, as the above lik says, it is not broken down by UV in the absence of photosensitizers. Jablonski and Chaplin staked their generalisations on psoriasis patients who had been treated with photosensitisers. As Bruce Ames wrote here "These observations suggest a new role for reduced folate in protection from ultraviolet damage and have bearing on the hypothesis that folate photodegradation influenced the evolution of human skin color".

The vitamin D side is even more clear cut. Confirming the (gold standard for medical advice) IoM report, a recent study found Race, genetics explained variations in 25-hydroxyvitamin D. It's got nothing to do with skin pigment, and so black Africans do not need extra vitamin D in north America or Europe. There is only one explanation left standing.

Ken said...

" dark skin has been under extremely high functional constraint in the tropics and high-UV areas for hundreds of thousands of years"

Tobias, dark skin does not correlate with UV intensity even in Sub Saharan Africa (Bushmen of the Kalahari). What it does correlate with is polygyny (and digit ratio). See here In Africa the hunter-gatherers are brown not 'black'. I agree that dark skin protects against infection, but high testosterone, such as would be selected for in polygyny, is immunosuppressive.

Tobus said...

@Ken: Tobias, dark skin does not correlate with UV intensity even in Sub Saharan Africa (Bushmen of the Kalahari)

I guess that depends on how you define "Dark skin". While there is certainly a wide range of pigmentation in Sub-Saharan Africa, "light-skinned" populations such as the San still have much darker skin than Europeans and East Asians, with reflectance levels comparable to the darkest South Asians.

I agree that a UV-only theory is fairly weak and circumstantial, and the mono/poly-gamy angle is not one I'd encountered before, so thanks for the link.

Jules said...

I also think that Scandinavians and others inbred for blue eyes. Estonians must really like blue eyes, since 98% of them have blue eyes.

I think that brown eyes were the first eye mutation. Most of the world has such a deep dark brown, that it's almost black. Sub Saharan Africans and East Asians for the most part, are an example of having nearly black or heavily pigmented irises.

The further away from the Black Sea, the darker the eyes. No one ever talks about light to medium brown eyes being a mutation of less melanin in the front of the iris. You can distinguish the pupil easily, unlike heavily pigmented nearly black eyes.

East Asians have the light skin, but not the light eyes. At most, they picked up some lighter browns, but not a lot. No one talks about lighter skinned people who did not obtain lighter eyes.

No one thinks about European Mediterraneans being hunter gathers that perhaps turned farmer. The basic deep genetics of Sardinia is a good example of this.

Instead, we get the whole Anatolian story from so many genetic sites. I doubt hunter gathers were totally in northern Europe and I doubt that southern Europeans are only Anatolian mixed with European. Instead I'd like to see if we have an ancient southern European hunter gatherer component.

I don't like Mediterranean as a group for southern Europeans. It leads people to faulty conclusions about southern Europeans, especially Italians. Having tested Italian and being extremely pale skinned, I can attest to the fact that we aren't all dark.

Mediterranean gives the impression of being related to north Africa. I came in with a fraction of a percent of any kind of north African markers and zero sub Saharan. Also very little middle eastern. 5% at most. I ran my data through Gedmatch.

I'm northern Italian and the variations on Gedmatch between the admixture programs were laughable. My genetics were European and Italian, but there were wild variations in my northern European component.

2014 to me will be yet more confusion and I doubt we will get clarity. I found genetic testing sites and Gedmatch to be more like astrology than contributing any real answers; the reason being that the answers are too complex.

Simon_W said...

Jules, the different admixture calculators at Gedmatch differ from each other because each project that created them used different population sets and varying numbers of components. That's why the components are not the same in every calculator. Also partly there were different methods used in the finding and definition of the components. But for instance Dodecad with its K12b and the Harappa Project arrived at very similar components, those from MDLP World-22 differ a little, obviously most of all because of the inclusion of ancient DNA. Eurogenes differs the most because of very high numbers of components and different methodolgy. It's far from being nonsense, but you have to bear the reasons for the differences in mind.

eurologist said...

Ken,

You are really grasping at straws, here. None of the studies you cited explain what we are are talking about, here, at any significant level.

Ken said...

Allow me, if I may, to quote "The intensity of UVA was ∼3-fold less than the maximum level in solar radiation. Thus, the observed rates of photodegradation are so low that a meaningful physiological impact of UVA or UVB in sunlight on 5-MTHF in the absence of photosensitizers seems unlikely, especially taking into account the integrated exposure to solar UV over an entire day or season rather than the maximum level during the day." here.

(My comment:Solar UV does not cause folic acid deficiency or cause it to become mutagenic.)

-----
"Powe and colleagues provide clear evidence that racial differences in serum 25-(OH)D are due to common genetic polymorphisms, and that bioavailable 25-(OH)D may be a better indicator for determining insufficiency. Thus, screening individuals for low vitamin D using the conventional serum 25-(OH)D measurement may lead to erroneous results." here.

(My comment: Africans' dark skin does not interfere with vitamin D synthesis.)
---

Tobias, the most polygynous place in Africa is Senegal, and it also has the darkest skinned population.

Michael J Hunter said...

Sorry for the multiple postings: trying to establish gmail and get send full information.

With the Neanderthal genome now published, for the first time, scientists have a rich new resource of comparative evolution. For example, recently, scientists have shown that humans and Neanderthals once interbred, with the accumulation of elements of Neanderthal DNA found in up to 5 percent in modern humans. Scientist have found evidence of accumulation of a Neanderthal DNA region found on chromosome 3 that contains 18 genes, with several related to UV-light adaptation, including the Hyal2 gene. Their results reveal this region was positively selected and enriched in East Asians, ranging from up to 49 percent in Japanese to 66 percent in Southern Chinese.

Neanderthal Introgression at Chromosome 3p21.31 was Under Positive Natural Selection in East Asians

http://m.mbe.oxfordjournals.org/content/early/2013/12/13/molbev.mst260.abstract

Jules said...

Hi Simon,

Okay, well, I was a little harsh there about Gedmatch. I do understand that you can't always pull apart recent and deep ancestry. Geno 2.0 and 23andMe enlightened me there. I'll keep in mind what you said about the different programs. I ran my 23andMe data through Gedmatch. I read the blogs associated with these programs and some are detailed in explanation and others are not. I'll run the ones you mentioned again and check them against each other. Thanks much. Happy New Year to all.

Matt said...

@ Dienekes, with respect to the "Ancient human genomes suggest three ancestral populations for present-day Europeans" paper, do you think it would be practical to use the mean admixing proportions given to "recreate" the ANE, WE and EEF populations, as per your "zombie" ancestral North Indian and ancestral South Indian populations?

http://dodecad.blogspot.co.uk/2011/05/more-zombies-ancestral-north-indians.html

Are there any statistical reasons why this would not be as valid?

Tobus said...

@Ken:the most polygynous place in Africa is Senegal, and it also has the darkest skinned population.

That may be so, but it doesn't imply causation. According to my sources some the darkest populations in Africa are in Mozambique, Cameroon ,Namibia, Chad, Tanzania, Malawi, Nigeria and Zaire (Dalton 2011). There is some crossover, but on the whole there doesn't seem to be any significant correlation between polygyny and pigmentation based on those two sources.

Simon_W said...

Jules, true, these Admixture calculators can't distinguish between recent and deep ancestry. Moreover a component called „North European“ for instance doesn't necessarily imply ancestry from northern Europe, since even pre-neolithic Iberians were strongly „Northern European“. Italians are known to have a very multiethnic past with various tribes and languages being present in pre-Roman times. On the other hand, they didn't mix much with other peoples since then, as their low international IBD-sharing shows, so they were more or less in place since then. A good knowledge of ancient history and archeology is certainly useful to help interpreting the results of an admixture analysis. Personally I was also very interested in the analysis of my Italian ancestry, from the Emilia-Romagna region. My conclusion so far being that my grandfather from this region seems to be closest to the Bergamo sample, but with relatively little North European admixture and a tendency towards Semitic peoples that was quite mysterious to me at first. But now I see that he's just a little closer to the „Stuttgart“ Early European Farmer than the north Italians from Bergamo are – which conforms well to the comparatively low incidence of blond hair in the Emilia-Romagna. Apparently the Celtic impact in this region was quite modest. I also analyzed my East Prussian grandmother's DNA sample with great interest, especially with regards to the percentage of Old Prussian ancestry. The „oracles“ are very useful for such purposes, but they have to be used with caution as well. I estimate her Old Prussian ancestry to be about 25%, so it's definitely present, but not as high as I had anticipated. Another amazing example of a successful application of the admixture calculators is from a distant English cousin of mine who was told a „family legend“ about some Roma roots of one of her forebears. I immediately doubted her story. But then I ran her DNA sample through the Dodecad calculators and I noted a slightly, but appreciably elevated level of the South Asian component. I can only conclude that her family legend must be right. But always remember that the components of different calculators are not the same even when their name is the same. What a result in components means, is best assessed by comparing it to the percentage levels of other populations. And for this purpose there are the associated oracles.

apostateimpressions said...

It seems that Neanderthals contributed genes that are still functional in some AMH, eg. for light adaptation.

Science Daily, Dec 18

quote:

Are there any advantages to the retention of Neanderthal DNA that favors modern humans? In a new article published in Molecular Biology and Evolution, authors Jin, et. al., present evidence for the accumulation of a Neanderthal DNA region found on chromosome 3 that contains 18 genes, with several related to UV-light adaptation, including the Hyal2 gene. Their results reveal this region was positively selected and enriched in East Asians, ranging from up to 49 percent in Japanese to 66 percent in Southern Chinese.

http://www.sciencedaily.com/releases/2013/12/131218100229.htm

apostateimpressions said...

Another, from Nov:

'Immune Gene' in Humans Inherited from Neanderthals, Study Suggests

A research group at Bonn University and international collaborators discovered a novel receptor, which allows the immune system of modern humans to recognize dangerous invaders, and subsequently elicits an immune response. The blueprint for this advantageous structure was in addition identified in the genome of Neanderthals, hinting at its origin. The receptor provided these early humans with immunity against local diseases. The presence of this receptor in Europeans but its absence in early men suggests that it was inherited from Neanderthals.

http://www.sciencedaily.com/releases/2013/11/131122084405.htm

Jules said...

Simon, I learned a lot in the two posts you have up. Many things are making sense. My father's family is from near Ferrara in Emilia-Romagna. They originated in Tuscany very long ago from what I understand. I came in with some Jewish ancestry also. I have no clue about that. Thanks for all the information about your family and Emilia-Romagna. I can't keep my ancestry straight anymore. I get such various accounts from family and genetically also. I normally come in Tuscan first. I'm having a hard time accounting for various northern European and Baltic results. It depends on recent or deep ancestry. One testing site does Caucasus and they did not have me there, only Tuscan and Greek. When I run my data through other programs the Tuscan/Northern Italian shows up as well as Greek and Caucasus. I think there may be things about my family I don't know and I've run into dead ends with research. I'm not sure you'll get this response. I've been having problem with my Google Account doing odd things. Thanks for the information. Very informative.

Simon_W said...

Jules, we're getting off the thread topic, I hope Dienekes bends the rules...

Distant roots of a certain lineage, e.g. of your purely male line of descent, hardly matter genetically. If you go back just five generations, to one of your g.g.g-grandparents, then that ancestor is just one of 32 g.g.g.-grandparents. On average he or she would have given you 1/32 of your DNA. This number would halve with every additional generation backwards. So you see, it's negligible. For this reason I've never quite understood the fasciniation for genealogy that some people have. In my opinion it suffices to know where your 8 great-grandparents were from. Or your 16 g.g-grandparents at most.

Northern European influence in Italy isn't abnormal at all. Every Italian has a decent bit of it, except for the Sardinians. Ötzi the Iceman didn't yet have it. So apparently it arrived later with tribes which came from central Europe. So in all likelyhood you don't have to consider recent northern European ancestry to account for this. But we don't have to guess, you can compare your percentage number with the averages of the various Italian subpopulations in the spreadsheet of the calculator (at least Dodecad does have spreadsheets), or you can look if the associated oracle suggests some admixture from a northern population.

I think you confuse admixture components and populations. Tuscans, Greeks and Northern Italians are populations. Caucasus on the other hand is an admixture component that's part of some calculators. The populations from the Caucasus are indicated more precisely with their name. So a calculator may tell you how much percent of the Caucasus component you've got. In a second step you can analyse your values with the associated oracle which compares them to populations and mixtures thereof.

The biggest difference between northern, central and southern Italy is, that the Caucasus component is comparatively weak in the north and gets constantly stronger towards the south. Associated with it is the West Asian component of other calculators.

A Jewish-like component in an oracle result really doesn't mean that you're part Jewish. Especially the Ashkenazi Jews are rather similar to southern Italians and Sicilians. According to the Dodecad K12b oracle they're like a blend of 88% Sicilians + 12% Samaritians. This near eastern shift of more southerly parts of Italy is the result of ancient contacts with Eastern Mediterranean and near Eastern peoples.

If I may ask, where is your mother's family from?

Guillaume Breteuil - Porlier said...

Face it: R1 lines are a European mirror for Ancient North Eurasian. Which makes sense, because we have clear evidence that the R lines are Ancient, north, and Eurasian. YEs ! R1b is about 40000 years in western Europe , there is no recent invasion because no mixed R1a-R1b the geographical split is extremely old before the ice age I see many stupidities about cooper age indo europeans etc.. non sens !

terryt said...

"I've never quite understood the fasciniation for genealogy that some people have. In my opinion it suffices to know where your 8 great-grandparents were from. Or your 16 g.g-grandparents at most".

Exactly. In fact at a generous 25 years a generation in 500 years you have over a million ancestors. Of course some of these will be repeats, and represent a level of inbreeding, but if humans have as many as 100,000 genes (probably a great overestimate) you have no genes from over 90% of those ancestors. five hundred years is not a particularly long time really.

Simon_W said...

It's a pity Jules doesn't reply. It would be interesting to know if the people around Ferrara are indeed Tuscan-like, or if his mother had brought in some central or south Italian admixture. I know some good reasons why the former might be true.