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Angela
10-05-16, 18:48
The link to this article from the Pritchard group is here:

Detection of human adaptation during the last 2000 years.

"http://biorxiv.org/content/early/2016/05/07/052084

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


Razib opines here:
http://www.unz.com/gnxp/the-2000-year-selection-of-the-british/

"Perhaps more interesting is that the authors detect continuous selection on height and pigmentation in their sample. Why height? I’ve been skeptical of some of the genetic arguments in Greg Clark’s A Farewell to Alms (http://www.amazon.com/exec/obidos/ASIN/0691141282/geneexpressio-20) (and have told Greg so), but, recent selection for height does seem to align with his idea that the English were particularly wealth and healthy over the past ~2,000 years. And, it also seems to support the suggestion of elite over-production, as presumably tall men would be more well represented among elites for both nutritional and genetic reasons."

"The results for pigmentation are intriguing. Some of the older signals don’t show up (e.g., SLC24A5 andSLC45A2). They’re either fixed, or near fixed, so where are the old haplotypes going to be to compare to? But intriguingly the selection around KITLG and OCA-HERC2 still seems to be occurring! Though the authors associate them with hair and eye color, the extreme tissue specific expression does not mean they have no effect on skin color. In the supplements they note that “In all 14 cases the derived allele is associated with either lighter pigmentation (i.e., lighter hair, skin, or eyes) or increased freckling.” Additionally, they state in the main text that “We speculate that recent selection in favor of blond hair and blue eyes may reflect sexual selection for these phenotypes in the ancestors of the British, as opposed to the longer-term trend toward lighter skin pigmentation in non-Africans, generally thought to have been driven by the need for Vitamin D production.”"

I speculated that this might have been the case when we saw the results for the samples representing the population overturn in Britain after the Neolithic. They didn't look like a blonde and blue eyed population, not that they're all blonde even now, even in the areas that are more "Anglo-Saxon".

That leads me to the fact that I'm not so sure that migration didn't have some effect, and climate as well. I'm aware that the AS part of the English genome is around 20-30% yes? That probably isn't enough to produce the change.

However, if the Anglo-Saxons, who seem to be the last major folk movement into Britain, were more represented in the elite groups, and were more blonde and blue eyed than the prior "Celtic" inhabitants, then, as a natural process in such situations that look would be associated with a higher social status, and so people would sexually select for it. These kinds of processes are the products of culture once perhaps more ingrained preferences like selection for "healthy" traits like symmetry of feature, clear skin, shiny hair, and perhaps certain anatomical features related to female and male hormone levels are considered.

In terms of light eyes I still think that more research has to be done into whether solar radiation plays a factor. Ireland has extremely high levels of light eyes. Yet, the ancient samples don't show particularly high levels of light eyes. I don't think it can be all down to AS gene flow, because there was much less of it there than in England. They're also more dark haired than the English from what I remember.

Razib seems convinced that the authors factored out the effects of migration.
I haven't yet tackled the Supplement, so I don't know.

Anyway, they're very persuasive that selection can occur much more quickly than was previously imagined, as the LP increase has shown.

It would be nice if they did the same sort of analysis for other parts of Europe.

A Norfolk L-M20
10-05-16, 21:02
I do feel that it might be a little presumptuous to assume that the British were less blonde and blue eyed previous the the 5th Century AD. We really don't yet know what sort of migrations and admixtures took place in SE Britain before then. POBI suggested that it detected a major late prehistoric admixture with a French population. Some people have pointed to Caesar's account of a recent Belgae migration from the area from North France to the Netherlands.

Fire Haired14
10-05-16, 21:57
Most of the natural selection they're detecting happened before 2,000 years ago.

Angela
11-05-16, 15:10
Most of the natural selection they're detecting happened before 2,000 years ago.

They're showing that the selection has been on-going, i.e. that the percentage of people carrying these traits in Britain has increased over the last two thousand years, something about which we had clues already given that the pigmentation of even Roman era samples we found were much more brown eyed than present percentages. You made the same point yourself on the Dienekes blog.

http://dienekes.blogspot.com/2016/05/natural-selection-in-britain-during.html

This is Dienekes' take on it: "But, while ancestrally the modern Briton is probably a descendant of the Britons of 2,000 years ago with some admixture from similar continental European groups, he is not the same, as (apparently) substantial genetic adaptation has continued to operate in Britain over the same period."

As to the timing of the first major change in Europe, he makes the same point I have been making for a long time on this blog:

"Depigmentation is a trait whose genetic architecture is as well as understood as any. The results of this study might surprise writers of decades and centuries past who supposed that the spectrum of pigmentation of modern Europeans was the result of admixture-in varying measure- between Xanthochrooi and Melanchrooi races of primordial antiquity. All indications seem to be that depigmentation of hair, skin, and eyes did not co-occur in such a hypothetical race, but rather in different parts of the Caucasoid range, only reaching a high combined frequency in northern Europe to form the distinctive physical type that is distinctive of the natives of that region. It would be quite interesting to see how these traits evolved in Fennoscandia and the Baltic, regions that sport an even higher depigmentation than the British Isles. Traditionally, these areas were viewed as refuges of the Xanthochrooi but it may very well turn out to be that for whatever reason selection has acted in that area as well, as it did in the Eastern European plain where rather dark (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3977302/)Bronze Age steppe groups gave way to rather light pigmented living eastern Slavs."

I'm afraid all of Genetiker's fantasizing about a "white" Villabruna man isn't going to change that fact. I have my doubts about his calls. Even if they're correct, however, I don't know how many times it has to be pointed out that pigmentation, like most human traits, depends upon the combination of many snps. You can have dark skinned blue eyed people. We've posted pictures of people from India on this blog who fit that profile. You can see them in America occasionally because of the mixture of races. Malcolm X was very dark but his nickname was "Red" as a young man because his hair was very reddish. Light eyed dark skinned people can also be seen.

https://s-media-cache-ak0.pinimg.com/236x/58/11/13/58111394d2ba36234f6dbac7bb2bbc88.jpg

https://s-media-cache-ak0.pinimg.com/236x/90/fe/08/90fe0824827ac2cce0ae53e83b6e122b.jpg

Of course, the argument could be made that these ancient people had some unknown genes for de-pigmentation. OK, if that's the case then the consensus view will have to change. However, if that's the case, why has there been such an incredible increase in these derived snps for de-pigmentation in "modern" populations? These snps, by the way, have been shown in lab experiments on fish to indeed control de-pigmentation. (Links to those studies can be found in the innumerable threads here about pigmentation.)

As to the whys and wherefores, no researcher is challenging the fact that in higher latitudes with lower levels of solar radiation, paler skin, at least, would come in very handy for allowing more absorption of Vitamin D and could be under selection. Whether lighter eyes and hair are implicated is unclear to me.

.One poster on Razib's blog made the point that there is evidence for a variety of hair colors in East Asia. I had never heard that, and there's no link to studies, so I can't verify that. However, I posted on this blog some reactions of Japanese people to American actresses. Hardly a scientific, representative sample, I know, but I opined at that time that I found it interesting that while the Japanese had a marked preference for pale skin, they did not find light hair and eyes at all attractive. For whatever reason, any "sexual" selection that was going on was different than what happened in Europe. Is it because their most recent "ruling elite" were dark haired and eyed?

Fire Haired14
11-05-16, 17:47
They're showing that the selection has been on-going, i.e. that the percentage of people carrying these traits in Britain has increased over the last two thousand years, something about which we had clues already given that the pigmentation of even Roman era samples we found were much more brown eyed than present percentages. You made the same point yourself on the Dienekes blog.

Maybe it has been ongoing or maybe it hasn't. We need ancient DNA and can't trust modern DNA. The accuracy of the method used is impressive but is still catching selection from before 2,000 years ago.


As to the whys and wherefores, no researcher is challenging the fact that in higher latitudes with lower levels of solar radiation, paler skin, at least, would come in very handy for allowing more absorption of Vitamin D and could be under selection. Whether lighter eyes and hair are implicated is unclear to me.

The theory that Light skin is adaption to high latitude, like theories about the origins of modern Europeans, have pretty much all been proven wrong by ancient DNA. None of the theories based on modern data I've heard about the origins of uniform light skin in Europe are correct. There must be another reason besides high latitudes. WHG lived in most of Europe for at least 7,000 years undisturbed, but didn't develop light skin. EEF did for 3,000 years and skin color alleles didn't change.


For whatever reason, any "sexual" selection that was going on was different than what happened in Europe. Is it because their most recent "ruling elite" were dark haired and eyed?

Bla bla. Don't worry not many researchers will give sexual selection or a grand white Bronze age elitism full credit. We have to consider sexual selection, but it's hard to believe every generation in every location for 1,000s of years would unanimously prefer pale pigmentation.

Geneticker is reanalyzing all of the ancient DNA data and posting the amount of reads. It looks like almost all the Red hair alleles in Motala HGs, Anatolia Neolithic, and Yamnaya are false. So, we're probably also seeing a rise in Red hair frequencies in Bronze age Europe, and especially in the British Isles and Scandinavia.

Angela
11-05-16, 19:27
Fire Haired14;479977]Maybe it has been ongoing or maybe it hasn't. We need ancient DNA and can't trust modern DNA. The accuracy of the method used is impressive but is still catching selection from before 2,000 years ago.


That's a vastly overgeneralized comment. It's also internally inconsistent. The accuracy of the method used is impressive but the results can't be trusted? ( You said the same on the Dienekes blog, btw.) You also posted on that blog that the ancient dna we do have shows that change has taken place since the Roman era but all of a sudden you've changed your mind? Of course we need a lot more ancient dna, but that doesn't mean we can't learn a lot from statistical algorithms applied to modern dna. The guys over at Eurogenes spend their lives doing that not only with regard to ancient dna but with regard to modern dna. Also, how do you think we know so much about the phylogeny of yDna "Y" lineages? It's all based on modern dna.


The theory that Light skin is adaption to high latitude, like theories about the origins of modern Europeans, have pretty much all been proven wrong by ancient DNA. None of the theories based on modern data I've heard about the origins of uniform light skin in Europe are correct. There must be another reason besides high latitudes. WHG lived in most of Europe for at least 7,000 years undisturbed, but didn't develop light skin. EEF did for 3,000 years and skin color alleles didn't change.



That is absolute bunk. No one has ever said that latitude is the only factor. However, any respectable scientist involved in genetics research would vehemently disagree with your statement. It also contradicts many statements you've made yourself in the past.

Just take a look at maps of skin color worldwide and the correlation with latitude. Use the darn search engine and find all the threads here with links to the papers that show reduced Vitamin D absorption in people with dark skins in areas of low solar radiation. Or perhaps you never read them.

As to the timing of these events, do you think humans can decide when a beneficial mutation is going to appear? People don't move into low sunlight areas and ipso facto they're going to get a beneficial light skin mutation. That's a total misunderstanding of how evolution and natural selection work. Mutations are RANDOM. If they're beneficial in a given environment there is selection for them. If they're really disadvantageous they'll disappear because the carriers will die. If they're neutral, no harm no foul. If they're just mildly disadvantageous they'll accumulate, especially if there's too much inbreeding. Accumulate enough of them and you'll get an effect on fitness, which may have happened with the Neanderthals.

In the move from Africa various mutations occurred which resulted in depigmentation. ONCE they had occurred, they were selected for because they were beneficial. The WHG were not black skinned like Nigerians today.

They didn't, however, have snps for derived SLC24A5 or SLC42A5. That was their bad luck because they might have been healthier given their environment. My speculation is that the SLC24A5 derived version was the result of a mutation in the Caucasus area, which is where a lot of older studies always placed the origin of the light eye allele. The SLC42A5 mutation might have taken place in that general area as well, although it may also have taken place among arming populations in central-Eastern Europe and then diffused from there.

Regardless, it was the misfortune of the WHG that they or their ancestors left for Europe before those mutations happened or before the spread of the mutations reached them. Once the derived versions arrived in Europe, or central Europe, those mutations, more helpful in northern areas of Europe than in Anatolia, increased in frequency.


Bla bla. Don't worry not many researchers will give sexual selection or a grand white Bronze age elitism full credit. We have to consider sexual selection, but it's hard to believe every generation in every location for 1,000s of years would unanimously prefer pale pigmentation.


Totally over generalizing and over simplifying AGAIN. As well as being disrespectful. I don't WORRY about any of this, because I don't give a darn one way or another. I'm not one of these Nordicist bigots who infest the amateur genetics field. The authors didn't say that it was definitely sexual selection based on social stratification that caused these recent changes and neither did I. To pretend that these things couldn't factor in at all is short sighted. Also, again, you don't understand how "sexual" preference works beyond the basic "cues" about health. It's not that people in different areas just decided one day to prefer "pale" skin. The point I was making is that if a group comes into power that "looks" a certain way, I absolutely GUARANTEE you that people will want to look like that, and people will find that trait attractive. That is human nature.

As for red hair, there's a whole science about it and about how it is connected with dark haired populations. I am not going to look it all up again. It's all on this blog in the various threads about pigmentation. Of course, it involves doing some actual reading.

Fire Haired14
11-05-16, 21:47
@Angela,

My "bla bla" wasn't directed to you. It was directed to anyone who would exaggerate the idea of a white elite in Bronze age Europe. I wasn't insulting you. I have reason to doubt the sexual selection or elitist thing. I understand your points, but still have doubts. I consider that theory but am more comfortable just saying we have no idea why it happened and not even mentioning sexual selection as a possibility.


Just take a look at maps of skin color worldwide and the correlation with latitude. Use the darn search engine and find all the threads here with links to the papers that show reduced Vitamin D absorption in people with dark skins in areas of low solar radiation.

Ok sure, I'm still not as convinced as you. I understand the evidence but don't think it's very convincing. I'm not ignoring it and saying it can't be true. When I say old theories have been proven wrong, I mean they thought because of high latitude light skin evolved in Paleolithic Europe. They were wrong. Others also said it was during the Neolithic, again they were wrong. It's possible that for 30,000 years straight humans in Europe were Brown skinned. A new circumstance, not high latitude, around 5,000 years ago could have caused that to change.


Once the derived versions arrived in Europe, or central Europe, those mutations, more helpful in northern areas of Europe than in Anatolia, increased in frequency.

Neolithic Central Europeans had the same frequency as Neolithic Anatolians. The change begins with Corded Ware.


You also posted on that blog that the ancient dna we do have shows that change has taken place since the Roman era but all of a sudden you've changed your mind?

I haven't changed my mind. We need more data from Iron age Europe. I'm just pointing out that with the small amount of data we have Iron age Britons had significantly more Brown eyes. I think most of the selection signals they're picking up occurred before 2,000 years ago. Lactose tolerance alleles for example in Iron age Poland and Britain were at modern frequencies. Some of the alleles they say have reason in frequency recently, have infact not risen in frequency, they are at the same frequency in all pre-historic and modern Europeans.

ThirdTerm
11-05-16, 22:21
http://www.nature.com/polopoly_fs/7.24538.1426765655!/image/1.17136.jpg_gen/derivatives/landscape_630/1.17136.jpg

The assumption of population continuity is necessary to infer natural selection based on temporal differences in allele frequency. Another study by Wilde et al. (2013) reached the same conclusion on the Ukrainians in the past 5,000 years. Wilde et al. (2013) found that strong selection favouring lighter skin, hair, and eye pigmentation has been operating in European populations over the last 5,000 years. They assumed that 63 ancient specimen from the Pontic-Caspian steppe dated from 6,500-4,000 years ago are directly ancestral to the modern-day Ukrainians without any significant population turnover.



Conversely, continuity between early central European farmers and modern Europeans has been rejected in a previous study (33). However, the Eneolithic and Bronze Age sequences presented here are ∼500–2,000 y younger than the early Neolithic and belong to lineages identified both in early farmers and late hunter–gatherers from central Europe (33). A plausible explanation for this is that the prehistoric populations sampled in this study are a product of admixture between in situ hunter–gatherers and immigrant early farmers during the centuries after the arrival of farming, and that this admixture was a major process shaping modern patterns of mtDNA variation (34) and possibly also the variability observed in European hair, eye, and skin color.


In Britain's case, population continuity did not exist in the last 2,000 years as the Anglo-Saxons from present-day Germany interbred with local residents, instead of replacing them wholly, after the departure of the Romans in 410 AD. It could be the Anglo-Saxons who introduced KITLG and OCA2/HERC2 to the Britons in the process of admixture and OCA2/HERC2 was found at a 100% frequency in the European hunter-gathers (hg I) analysed by Matheison et al. (2015). A copy of the OCA2/HERC2 gene was present in one of the Bronze Age samples from the British Isles (Cassidy et al. 2016) but all Bronze Age samples belonged R1b and had brown eyes. With the Anglo-Saxon migrations, the frequency of OCA2/HERC2 must have significantly increased in Anglo-Saxon Britain, while it was quite rare in the ancient Britons. The SLC45A2 mutation was already present in Celtic Britain, which is a very common light skin mutation in modern European populations (97%).



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


Natural selection also could have played a role in the selection of sexual partners and women may have preferred tall and blonde men of Scandinavian decent or vise versa, especially after the establishment of Norse settlements in the 9th century in such places as East Anglia, Yorkshir and Dublin.



Evidence of selection on height
We also tested for selection on complex traits. The best-documented example of this process in humans is height, for which the differences between northern and southern Europe have been driven by selection36. To test for this signal in our data, we used a statistic that tests whether trait-affecting alleles are both highly correlated and more differentiated, compared to randomly sampled alleles37. We predicted genetic heights for each population and applied the test to all populations together, as well as to pairs of populations (Fig. 4). Using 180 height-associated SNPs38 (restricted to 169 for which we successfully obtained genotypes from at least two individuals from each population), we detect a significant signal of directional selection on height (P= 0.002). Applying this to pairs of populations allows us to detect two independent signals. First, the Iberian Neolithic and Chalcolithic samples show selection for reduced height relative to both the Anatolian Neolithic (P= 0.042) and the central European Early and Middle Neolithic (P= 0.003). Second, we detect a signal for increased height in the steppe populations (P = 0.030 relative to the central European Early and Middle Neolithic). These results suggest that the modern South–North gradient in height across Europe is due to both increased steppe ancestry in northern populations, and selection for decreased height in Early Neolithic migrants to southern Europe.

MOESAN
12-05-16, 15:23
I foud this urvey a bit presomptuous in its conclusions!!!
1- I don't like the "british" global concept, it's a kind of negation of ancient and recent history.
2- we lack solid samples from ancient times to check the consluions obtained upon modern populations for the most.
3- if Siluri were described as darker than other Brittons, it show some Brittons were lighter! ( recall the Caledonians!) If Antiquity historians were not anthropologists, what reduce the accuracy of their observations, they had e nough eye to see some diifferences, even if they were unable to quantify them seriously. As a whole we know ancient "Brittons" or considered as Brittons, were not a completely homogenous population.
4- I thinkt he A-Sx imput is underrated as a whole in some regions; all the way, the serious maps concerning pigmentation of hair and my own observations in UK show clearly the neat imput of diverse Germany, as a whole and in details, visible until the 1960's.
5- the ligtening in pigmentation has been reinforced by Germanics, but was begun before them in some parts of UK.
6- social selection can play a role: lighter associated to higher social level (the winners!), and higher social level people mating more (males the most) with results upon genes poles.
7- I have hard work to swallow all thise quick and late selections upon people 's genomes at a time where naturla environmental pressure had - I think - less and less imput on Mankind. We can always imagine genes selected by hazard at the same time as other genes more important for the health (proximity on chromosome?) ? Not impossible. But
which plague or which climatic event has produced these conditions? I think rather in populations moves from very different regions at first, whic could explain selection moregradual in other places (always I thin into South-East-Baltic-Western Steppes?.
8- the samples we have today for yamnaya and others are surely elites samples... we make too much conslusions based upon elites, males for the most, I suppose.

MOESAN
12-05-16, 15:26
Sorry for my "cuckoo eggs"; I did not reread myself seriously. Beg your pardon!

Angela
12-05-16, 18:13
http://www.nature.com/polopoly_fs/7.24538.1426765655!/image/1.17136.jpg_gen/derivatives/landscape_630/1.17136.jpg

The assumption of population continuity is necessary to infer natural selection based on temporal differences in allele frequency. Another study by Wilde et al. (2013) reached the same conclusion on the Ukrainians in the past 5,000 years. Wilde et al. (2013) found that strong selection favouring lighter skin, hair, and eye pigmentation has been operating in European populations over the last 5,000 years. They assumed that 63 ancient specimen from the Pontic-Caspian steppe dated from 6,500-4,000 years ago are directly ancestral to the modern-day Ukrainians without any significant population turnover.

I agree with that criticism of Wilde et al. As to this paper, I still haven't pored over the supplement, although it's on my to do list, so I'm not sure if their claim that they've totally factored out the effect of population flow is persuasive or not. You obviously think not, I take it.


[QUOTE]In Britain's case, population continuity did not exist in the last 2,000 years as the Anglo-Saxons from present-day Germany interbred with local residents, instead of replacing them wholly, after the departure of the Romans in 410 AD. It could be the Anglo-Saxons who introduced KITLG and OCA2/HERC2 to the Britons in the process of admixture and OCA2/HERC2 was found at a 100% frequency in the European hunter-gathers (hg I) analysed by Matheison et al. (2015). Natural selection also could have played a role in the selection of sexual partners and women may have preferred tall and blonde men of Scandinavian decent or vise versa, especially after the establishment of Norse settlements in the 9th century in such places as East Anglia, Yorkshir and Dublin.


Overall genomic similarity would have been high between the "Celts" on the one side and the Belgae and Anglo-Saxons on the other, although these snps related to "appearance" phenotypes are a very small percentage of total genomic variation, so there could have been differences between the groups. However, if the genomes of the post Neolithic population that entered Britain are any indication, some of them did have the alleles for light skin and blue eyes. It's just that the frequency was lower. Of course, these sample numbers are low.

See page 69 of the supplement from Cassidy et al, Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome.
http://www.pnas.org/content/suppl/2015/12/23/1518445113.DCSupplemental/pnas.1518445113.sapp.pdf

As to sexual selection, I doubt that women were doing the selecting. Unfortunately, for most of human history women have not had the power to choose their mates.

Tomenable
25-05-16, 07:50
Eastern European plain where rather dark Bronze Age steppe groups gave way to rather light pigmented living eastern Slavs.

Fire Haired has made nice spreadsheets with data on prehistoric pigmentation, and they show that most of Bronze Age steppe groups were actually light-pigmented. The only rather dark pigmented steppe groups were the Yamnaya and Catacomb samples, while samples from most of other steppe cultures were rather light-pigmented. Especially Bronze Age steppe groups considered to be Proto-Indo-Iranic (i.e. those dominated by R1a-Z93) were light-pigmented.

So Dienekes is wrong.

By the way - even though Yamnaya were relatively dark, the earlier Samara Hunter-Gatherer (the one with R1b) was light-pigmented. And also according to Fire Haired's spreadsheet, around 10% of Yamnaya people were actually blondes. This is still a large percent (larger than in most of Non-European populations today). In ENF-descended cultures such as Remedello, 100% of the people were black-haired. Yamnaya, on the other hand, had many blonde and brown guys.

Angela
25-05-16, 14:46
Fire Haired has made nice spreadsheets with data on prehistoric pigmentation, and they show that most of Bronze Age steppe groups were actually light-pigmented. The only rather dark pigmented steppe groups were the Yamnaya and Catacomb samples, while samples from most of other steppe cultures were rather light-pigmented. Especially Bronze Age steppe groups considered to be Proto-Indo-Iranic (i.e. those dominated by R1a-Z93) were light-pigmented.

So Dienekes is wrong.

By the way - even though Yamnaya were relatively dark, the earlier Samara Hunter-Gatherer (the one with R1b) was light-pigmented. And also according to Fire Haired's spreadsheet, around 10% of Yamnaya people were actually blondes. This is still a large percent (larger than in most of Non-European populations today). In ENF-descended cultures such as Remedello, 100% of the people were black-haired. Yamnaya, on the other hand, had many blonde and brown guys.

I'm not quite sure what you mean by light-pigmented. Do you mean presumed to have pale skin because they are derived for both SLC24A5 and SLC42A5, or do you mean that in addition that they were blonde haired and blue eyed?

Could you please provide a link to Fire-Haired's sheet? My recollection is that the Yamnaya and succeeding Catacomb Culture people were darker than any modern Europeans. Also, I seem to recall that the steppe people who are "lighter" are separated from them by about 1000 years, yes? They are certainly not their contemporaries. Perhaps there was time enough for some selection to operate on them? These much later steppe people also have a chunk of Anatolian farmer, don't they? Perhaps they picked up some lighter genes when they picked up that and their Z93 at the same time. You do think Z93 was all the way to the west, yes? After all, we already had a predicted light skinned, light haired and blue eyed sample in the 5th millennium BC Neolithic in Hungary as per Gamba et al.

http://www.nature.com/ncomms/2014/141021/ncomms6257/images/ncomms6257-f3.jpg

By the way, I chanced upon a blog post by Genetiker where he calls into question the fact that the SHG had derived snps for light pigmentation. He claims only 1/5 or 6 of the calls came in derived, and they were near the end of the sequence where damage is most common. Do you have a link to that? I can't find it again, and I'd like to check if he took another look at those later steppe samples as well.

Regardless, your points have to do with people all the way to the east. What does that have to do with the phenotypes of the people who went to Britain and whether they were darker than modern Britons? We of course know the pigmentation of modern Britons. We don't have many Bronze Age British samples, but the ones we do have are a bit darker than modern people. Now, an obvious thought is that perhaps the British were "lightened" by the "Anglo-Saxon" migrations. The authors maintain that their algorithm factors out the effect of migration. (Of course, how do we know that the Anglo-Saxons of the time were in fact "lighter" than the "Celts" of the British Isles, as we don't have any samples of them? After all, that Bronze Age warrior found in Poland was claimed to have "darker" skin than modern Poles.) I haven't had time to pore over the equations in the Supplement. Have you taken a look at them? Are they persuasive?

Fire Haired14
25-05-16, 19:26
My Spreadsheet. (https://docs.google.com/spreadsheets/d/1xe9sgt0PSt6cUQ3cYp14foBoaVGsOKZBmmHJoKz0HB0/edit#gid=1800275085)
I only include results from Geneticker that got 5 or more reads.

Angela
25-05-16, 20:50
My Spreadsheet. (https://docs.google.com/spreadsheets/d/1xe9sgt0PSt6cUQ3cYp14foBoaVGsOKZBmmHJoKz0HB0/edit#gid=1800275085)
I only include results from Geneticker that got 5 or more reads.

Thanks.

Someone sent me the link.

I think this is the latest Genetiker post on the snps in your chart. Is this the one you used?
https://genetiker.wordpress.com/2015/03/07/phenotype-snps-from-prehistoric-europe/

This is what he shows for Motala, for instance, for SLC24A5:


Motala HG I0012 3/3
Motala HG I0014 3/3
Motala HG I0015 0/1
Motala HG I0016 1/3
Motala HG I0017 8/8

This is what he shows for Motala for SLC42A5:Motala HG I0011 6/6
Motala HG I0012 5/5
Motala HG I0013 0/3
Motala HG I0014 10/20
Motala HG I0015 21/21
Motala HG I0017 4/13

What I remembered reading had to do with rs1805007 connected to red hair.

It was in the comments to this post.
https://genetiker.wordpress.com/2016/05/05/phenotype-snps-from-ice-age-europe/

Fire Haired14
25-05-16, 22:10
Thanks.

Someone sent me the link.

I think this is the latest Genetiker post on the snps in your chart. Is this the one you used?
https://genetiker.wordpress.com/2015/03/07/phenotype-snps-from-prehistoric-europe/

I use that link and a few others.

Fire Haired14
25-05-16, 22:34
Also, I seem to recall that the steppe people who are "lighter" are separated from them by about 1000 years, yes?

Catacomb is contemporary to EEF/Steppe admixed groups from Central Europe and was darker. It's possible Central European Corded Ware and Bell Beaker emerged from EEF/Steppe hybrids who had existed in Ukraine or further West since before 3000 BC, which would make them contemporary to Yamnaya. We don't know if that's the case so we have to treat them as 1,000 years younger than Yamnaya. If they were around before 3000 BC, they still could have been dark like Yamnaya.


So Dienekes is wrong.

Dieneks was referring to Yamnaya and Catacomb. The lighter pigmented EEF/Steppe hybrids formed in the Western edge of the "Steppe" or even Central Europe. Most of the "Steppe" was inhabited by darker people. The lighter ones weren't pure Steppe, all of them were at least 20% EEF(with minor WHG), and so if anything "Steppe" people are best represented by the darker ones.

All Dienekes is doing is pointing out that there was no ultra Pale/rainbow race of humans in Pre-Historic Europe who contributed the most to Swedes and least to Sicilians, and can explain Pale/rainbow coloring in Europe today, like what some used to think. Instead evolution is the source. This is very true. If no evolution occurred Swedish would be as dark as Armenians. 80-90% of their ancestry is Steppe and EEF, both of whom had the same pigmentation markers as modern Middle Easterners.


By the way - even though Yamnaya were relatively dark, the earlier Samara Hunter-Gatherer (the one with R1b) was light-pigmented.

It's possible some Mesolithic groups like the Motala HGs were pretty pigmented, but they're probably not an important source for modern Europeans. The picture has already been painted. We have good idea what happened. The fact is Yamnaya, and even Corded Ware and Bell beaker, were swarthier than their descendants. Something changed. We shouldn't be looking for a Pale race, but instead why evolution caused Pale pigmentation to grew in frequency.


And also according to Fire Haired's spreadsheet, around 10% of Yamnaya people were actually blondes. This is still a large percent (larger than in most of Non-European populations today). In ENF-descended cultures such as Remedello, 100% of the people were black-haired. Yamnaya, on the other hand, had many blonde and brown guys.

No, Yamnaya was dark like Middle Easterners. I guess maybe not like African-admixed Arabians and South Asian-admixed Iranian, but maybe like Assyrians or Armenians or Turkish. They would have been an interesting looking people unlike anything today, because they'd be swarthy like Middle Easterners but have very differnt and European-like facial features.

Angela
26-05-16, 00:07
Just to clarify, the quote about Dienekes being wrong was Tomenable's, not mine.

In terms of "lighter", more recent steppe people, I was talking about Sintashta.

My point about Genetiker's link is that he's showing a lot less than 5 calls for derived snps in a good number of those Motala samples.

Moi-même
26-05-16, 00:30
The fact is Yamnaya, and even Corded Ware and Bell beaker, were swarthier than their descendants. Something changed. We shouldn't be looking for a Pale race, but instead why evolution caused Pale pigmentation to grew in frequency.

It may not be evolution, it may just be a few families, too inbreed, who happen to have a higher rate of light skin, light hair, light eyes. Even if they accomplish a tenth of what Ginges Khan did, maybe even just a hundredth, the idea that light = elite was born. Thus low class families who happen to get a light kid will spoil them rotten, at the expense of the swarthy ones, in hope to get a better social standing for them and their descendants. In turn, they will often get the best spouse as these elite look alike are highly sought after. And the elite, who probably wasn't so light to begin with would do the same to keep ahead, until a few thousand years later, light skin, hair and eyes become the new normal.

Fire Haired14
26-05-16, 01:31
Just to clarify, the quote about Dienekes being wrong was Tomenable's, not mine.

I know. I mixed up the quotations.


In terms of "lighter", more recent steppe people, I was talking about Sintashta.

Corded Ware was also lighter. They didn't live in the Steppe but immigrated from there to Central Europe, so i count them as Western Steppe.


My point about Genetiker's link is that he's showing a lot less than 5 calls for derived snps in a good number of those Motala samples.

The ones who didn't get 5 calls got mostly derived alleles. Motala_Hgs were mostly derived fore both SLC42A5 and SLC24A5.

Fire Haired14
26-05-16, 01:31
It may not be evolution, it may just be a few families, too inbreed, who happen to have a higher rate of light skin, light hair, light eyes. Even if they accomplish a tenth of what Ginges Khan did, maybe even just a hundredth, the idea that light = elite was born. Thus low class families who happen to get a light kid will spoil them rotten, at the expense of the swarthy ones, in hope to get a better social standing for them and their descendants. In turn, they will often get the best spouse as these elite look alike are highly sought after. And the elite, who probably wasn't so light to begin with would do the same to keep ahead, until a few thousand years later, light skin, hair and eyes become the new normal.

You just described a way in which evolution can occur. We don't know how the evolution happened but it did.

LeBrok
26-05-16, 04:31
It may not be evolution, it may just be a few families, too inbreed, who happen to have a higher rate of light skin, light hair, light eyes. Even if they accomplish a tenth of what Ginges Khan did, maybe even just a hundredth, the idea that light = elite was born. Thus low class families who happen to get a light kid will spoil them rotten, at the expense of the swarthy ones, in hope to get a better social standing for them and their descendants. In turn, they will often get the best spouse as these elite look alike are highly sought after. And the elite, who probably wasn't so light to begin with would do the same to keep ahead, until a few thousand years later, light skin, hair and eyes become the new normal.
So far all points to the environmental selection of light skin due to northern climate, especially cloudy north of Baltic Sea than to sexual or cultural selection. If it was a strong sexual and cultural selection we would have had all world white and blond by now.

Fire Haired14
26-05-16, 13:10
So far all points to the environmental selection of light skin due to northern climate, especially cloudy north of Baltic Sea than to sexual or cultural selection. If it was a strong sexual and cultural selection we would have had all world white and blond by now.

I don't think any new evidence has come back supporting that theory, besides the Moatla_HGs(extinct Northern population who was pretty pale). The change in pigmentation occurred in all of Europe, the Northern parts. We have to be looking for reasons as to why today 70% in Spain and 90% in Italy have SLC42A5 while just 5,000 years ago 20% of other their ancestors did.

MOESAN
26-05-16, 14:05
Some faimilies of People had always been living at the edges of sub-boreal climates, before, during and after LGM: why general depigmentation did not occur sooner in these populations and why it occurred (when? I don't know) only in someones of them?
It's true, as a whole we can say the principal skin depigmentation occurred with diverse mutations in all the current populations under the "caucasian" or "europoïd" and "north-mongoloid" umbrella (except Inuits: why here too?). The additive depigmentation concerning hairs and eyes + some slight one for skin concerned only well determined populations before historic moves brought some mess: I fear we don't have all the clues and some of us ignore some anthropologic facts; by the way, whay are Western irishmen paler for skin but darker for hairs than Eastern Englishmen? Western Norwegians are less often blond than other Scandinavians, Saami too, Eastern Finns too and so on. And the Germanics trail for blond hairs is easy to follow in today Europe (before big erosion of late days) and they oppose themselves even to Slavs and Celts for that....
I'm not satisfied by the today explanations I red, none of them, so I wait.
I hope I shall not dead before!

LeBrok
26-05-16, 16:18
I don't think any new evidence has come back supporting that theory, besides the Moatla_HGs(extinct Northern population who was pretty pale). The change in pigmentation occurred in all of Europe, the Northern parts. We have to be looking for reasons as to why today 70% in Spain and 90% in Italy have SLC42A5 while just 5,000 years ago 20% of other their ancestors did.The evidence, is the ongoing process till our times. The epicenter of it is around Baltic Sea, the cloudiest place in Europe. The place with least UV radiation. The clue is that it happened in farmers societies the most. In Europe and in East Asia likewise (North China, Korea and Japan). Some Asians are as pale as Irish, but by means of different mutations. This should give you a clue that white skin is important in these climates for farmers. Other clue is that HGs of north are much lighter than HGs of south (please don't post pictures of suntanned Inuits). The clue is that UV radiation and colour of skin affects vitamin D production. The clue is that HGs of north get some of it from eating raw liver. The clue is that white people in hot climates get skin cancer much faster than people with darker skin.
Put these clues together to understand the big picture.

LeBrok
26-05-16, 16:21
Some faimilies of People had always been living at the edges of sub-boreal climates, before, during and after LGM: why general depigmentation did not occur sooner in these populations and why it occurred (when? I don't know) only in someones of them?
It's true, as a whole we can say the principal skin depigmentation occurred with diverse mutations in all the current populations under the "caucasian" or "europoïd" and "north-mongoloid" umbrella (except Inuits: why here too?). The additive depigmentation concerning hairs and eyes + some slight one for skin concerned only well determined populations before historic moves brought some mess: I fear we don't have all the clues and some of us ignore some anthropologic facts; by the way, whay are Western irishmen paler for skin but darker for hairs than Eastern Englishmen? Western Norwegians are less often blond than other Scandinavians, Saami too, Eastern Finns too and so on. And the Germanics trail for blond hairs is easy to follow in today Europe (before big erosion of late days) and they oppose themselves even to Slavs and Celts for that....
I'm not satisfied by the today explanations I red, none of them, so I wait.
I hope I shall not dead before!
That's right, the connection of light eyes and hair to light skin is not well understood. East Asians have pale skin, though other features are black like eyes and hair. On the contrary, some black skin people have blue eyes and blond hair (in childhood).

MOESAN
26-05-16, 19:05
For I think phoenotypes show (before going in genes analysis)
- we have mutations having favorized only skin depigmentations, in diverse poplations. (I would be very interested in knowing what is the genetic basis of the Khoisans skin colour, btw)
- mutations for light eyes without effect upon hair; but skin seems slightly lighter. Apparently disjoncted from hair and skin pigmentation. if I rely on genetics tudies.
- mutations seemingly involved in SLIGHT (additive) depigmentation of skin and STRONG depigmentation of hair and eyes.
- red hair is an other thing and freckling in not a neutral thing concerning pigment density, I think (it seems it never stroke the most of the scientists in their appreciation of lmight skin)
&: at the genetic level, close phoenotypes could be caused by different mutations, this is over my capacity of control.

in some Australoid people a blond hair seems associated to very dark eyes and very dark skin! So nothing in common with some Asiatic populations (Mongols, Turks of Steppes, where individuals show the "kit" of lighter skin, hair and eyes as in some Europeans. I say lighter than the most of their brethren, not everytime lilly white skin.

Tomenable
26-05-16, 21:51
My Spreadsheet. (https://docs.google.com/spreadsheets/d/1xe9sgt0PSt6cUQ3cYp14foBoaVGsOKZBmmHJoKz0HB0/edit#gid=1800275085)
I only include results from Geneticker that got 5 or more reads.

Fire Haired,

I rely on the older version of your spreadsheet, which included also data on blonde hair:

(do you now think this data is not reliable - is it why you removed it from the new version?):

Hair colours from the old version: http://s24.postimg.org/l49x5dt79/Hair_Colours_by_Culture.png

http://s24.postimg.org/l49x5dt79/Hair_Colours_by_Culture.png

Some of this data (e.g. Xiaohe mummies) was based on pigmentation from preserved hair, not from DNA.

But you've also removed this data which was based on visible pigmentation of well-preserved mummies.

Fire Haired14
26-05-16, 22:38
Fire Haired,

I rely on the older version of your spreadsheet, which included also data on blonde hair:

(do you now think this data is not reliable - is it why you removed it from the new version?):



Some of the results are unreliable. The red hair results are especially unreliable, because most got few reads on MC1R SNPs. I still have Hirisplex results here (https://docs.google.com/spreadsheets/d/1WN9qwNyju93dVXxkTMaYbzT4cBdMq9wZF-mIe1aMMcQ/edit#gid=603201826). These are more accurate. I used the same interpretation of results I do on modern populations, and the results for moderns made a lot of sense. That spreadsheet isn't updated either, I'll update it later and then I'll add it to my main spreadsheet.

This summary gives all the info you would need........
Paleo-Meslo West Europeans uniformly Black and Dark Brown. Mesol Russia and Sweden had Light Brown and Blonde in the mix. Neolithic Turkey/Europe and Bronze age Russia did to but at a lower frequency. A rise in frequency of Light Brown/Blonde and first appearance of Red in Bronze age Central Europe+Central Asia. A rise in frequency of Light Brown/Blonde in all of modern Europe after 2000 BC and a rise of Red hair in the British Isles and Scandinavia after 2000 BC.

Mesolithic Russia and Sweden are unique in that it looks like they could have been pigmented the same as modern Northern Europeans but it evolved independently in them. In 3000 BC most of Europe though was pigmented like the Middle East, then things changed very quickly.


Some of this data (e.g. Xiaohe mummies) was based on pigmentation from preserved hair, not from DNA.

But you've also removed this data which was based on visible pigmentation of well-preserved mummies.

I'll add that later.

MOESAN
27-05-16, 00:20
@FireHaired
Thanks for the work of sharing info you do (as do others, as Angela, Tomenable and ...
It is this quick change around the 2000 BC (I 'm not to confident about too precise dates, so it could have begun a bit earlier: 3000?) which push me to think only migrations could be responsible for so a revolution in North-West, and not a process of natural selection; we have to find unknown population in unkown place which could have underwent this selection of depigmentation genes for hair (and eyes) certainly more by isolation/bottleneck/founder effect than by natural pressure. I explained myself above.

MOESAN
27-05-16, 00:36
In fact I wrote faster than I was thinking.
Natural selection could have played a role, but not in the Isles, not between 2000 and 0 BC, not between 0 and 1000 AD. This natural selection could have stroke more than a population, rather in North and not too quickly, if these populations were in "pools of mating" were existed already the mutation(S), even if the first mutation(S) appeared at low level more southernly. But as other Northern populations do not show this depigmentation, we can very well imagine relatively isolated pôpulations at some stage of chronology.
I still favour diverse populations but settled between Baltic and North Western Steppes. (diverse mutations, but promoted by similar climate and environment, we know there blue and blue eyes, and blonds and blonds, as we say in french)

LeBrok
27-05-16, 01:43
For I think phoenotypes show (before going in genes analysis)
- we have mutations having favorized only skin depigmentations, in diverse poplations. (I would be very interested in knowing what is the genetic basis of the Khoisans skin colour, btw)
- mutations for light eyes without effect upon hair; but skin seems slightly lighter. Apparently disjoncted from hair and skin pigmentation. if I rely on genetics tudies.
- mutations seemingly involved in SLIGHT (additive) depigmentation of skin and STRONG depigmentation of hair and eyes.
- red hair is an other thing and freckling in not a neutral thing concerning pigment density, I think (it seems it never stroke the most of the scientists in their appreciation of lmight skin)
&: at the genetic level, close phoenotypes could be caused by different mutations, this is over my capacity of control.

in some Australoid people a blond hair seems associated to very dark eyes and very dark skin! So nothing in common with some Asiatic populations (Mongols, Turks of Steppes, where individuals show the "kit" of lighter skin, hair and eyes as in some Europeans. I say lighter than the most of their brethren, not everytime lilly white skin.
There is possible explanation, I think, in gene expression function. We know that all the genes are not expressed all the time. Different genes are expressed in different body parts and expression or lack of it also changes with time, especially during growth of young body. Hypothetical example: We could suppose that if light skin gene, allele of low pigmentation, is expressed in skin but not expressed in eyes, we could get a person of light skin and brown eyes. Conversely it could be expressed in both giving light skin and blue eyes. And to make the matter less transparent, it is usually a combination of many genes being expressed or not in eyes, skin, or even hair producing cells.

MOESAN
27-05-16, 15:07
Yes, Lebork: more than a biallelic gene, in more than a locus, with possible interaction (additive?). But the expressivity or "penetrance" is surely a result of other genes actions, not hazard (I don't say you think it was "hazard", but I prefer precise it). That said, it seems that light hair+light eyes+ slightly lighter skin is a or more than a "kit" distinct from the more spred light skin mutations. It's complicated and I satisfy myself with statistical phoentypic results, by cause of lack of knowledge at the detailed genetic level. Whe have seen the progress of scientific knowledge, coming to debuke ancient erroneous dogma (sometimes creating new ones!). Good afternoon. Endervezh vad deoc'h.

Angela
27-05-16, 17:31
Just to clarify something about the paper. They are discussing only the period of the last 2000 years, and they claim that there is indeed a difference in pigmentation in British populations during that period, with the population becoming "fairer".

We don't totally need to take their word for it. Although the sample size is small, we do have Bronze Age British samples, and they are significantly more brown eyed, for example, than current populations. As I and others have mentioned, an obvious alternative to continuing evolution might be the Anglo-Saxon invasions. The issue there is that they insist that their algorithms factor that out. Has anyone picked that apart to see if they're right?

The other issue is that we don't know what the majority of Anglo-Saxons looked like at the time. We have a Bronze Age Polish warrior who is supposedly darker than modern Poles, although to my knowledge no actual dna has been released.

All of that said, I think there is a problem with the concept of continuing evolution for modern populations in terms of pigmentation, given the changes in diet, and particularly in Vitamin D enriched foods and modern medications.

MOESAN
28-05-16, 22:56
...
All of that said, I think there is a problem with the concept of continuing evolution for modern populations in terms of pigmentation, given the changes in diet, and particularly in Vitamin D enriched foods and modern medications....

If I understand well your thoughts, I agree.
I red so often fanciful conclusions of SOME scientists (young ones having something to prove soon??? or people addict to scoops and buzz?) with conclusions I'm tempted to qualify as "schoolish", at least very simplistic, spite preparation technical works of high quality.
I can mistake, evidently. But natural selection of every kind needs the most often some time to definitively promote genes of low frequency. It's so complicated, sometime, as we can see with considered "letal" genes remaining in populations after generations and generations. I cannot figure out any plague or other kind of pressure justifying so dramatical selection, thousand of years after the apparition of the mutated genes, and producing effects at so recent times. I don't buy it, to date, before other proofs. We see today populations living in same environments since 4000 or 5000 years at least with some intermatting - so possibilities to exchanges genes for selection - and globally remaining very differently pigmented (without speaking of other traits).
If natural selection, I would rather prefer older times when Mankind was less equiped against environment. Sure, I can mistake.

MOESAN
28-05-16, 23:01
I add:
the samples are still very tiny for Britain Ireland, and we cannot be sure they are good examples of basic populations. only the christian era seems providing us big cimetaries with almost all the population, after the Dark Ages, I think.

jgviv
21-08-16, 12:37
Very interesting the difference in such a small territory