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Sile
15-03-15, 01:52
http://biorxiv.org/content/early/2015/03/13/016477.full-text.pdf+html

Maciamo
15-03-15, 09:28
Thanks for posting. Including at least the abstract would be nice instead of just posting a raw link, so we know what it's about. This paper reviews particular genes related to the physical traits and adaptation to the environment, including eye colour, skin pigmentation, hair thickness, vitamin D levels, immune system, body height, lactase peristence and lipid levels (influencing BMI and obesity risk).

Abstract

The arrival of farming in Europe beginning around 8,500 years 1 ago required adaptation to new environments, pathogens, diets, and social organizations. While evidence of natural selection can be revealed by studying patterns of genetic variation in present-day people1-6, these pattern are only indirect echoes of past events, and provide little information about where and when selection occurred. Ancient DNA makes it possible to examine populations as they were before, during and after adaptation events, and thus to reveal the tempo and mode of selection7,8. Here we report thefirst genome-wide scan for selection using ancient DNA, based on 83 human samples from Holocene Europe analyzed at over 300,000 positions. We find five genome-wide signals of selection, at loci associated with diet and pigmentation. Surprisingly in light of suggestions of selection on immune traits associated with the advent of agriculture and denser living conditions, we find no strong sweeps associated with immunological phenotypes. We also report a scan for selection for complex traits, and find two signals of selection on height: for short stature in Iberia after the arrival of agriculture, and for tall stature on the Pontic-Caspian steppe earlier than 5,000 years ago. A surprise is that in Scandinavian hunter-gatherers living around 8,000 years ago, there is a high frequency of the derived allele at the EDAR gene that is the strongest known signal of selection in East Asians and that is thought to have arisen in East Asia. These results document the power of ancient DNA to reveal features of past adaptation that could not be understood from analyses of present-day people.


Here are some of the genes and alleles studied. I have inserted the links to SNPedia for easy reference. Note that rs7940244 wasn't on SNPedia, but I found a proxy in the same gene.

HERC2 (rs12913832 (http://www.snpedia.com/index.php/Rs12913832) - eye color)
SLC24A5 (rs1426654 (http://www.snpedia.com/index.php/Rs1426654) - skin pigmentation)
SLC45A2 (rs16891982 (http://www.snpedia.com/index.php/Rs16891982)- skin pigmentation)
LCT (rs4988235 (http://www.snpedia.com/index.php/Rs4988235)- lactase peristence)
NADSYN1 (rs7940244 (http://www.snpedia.com/index.php/Rs7944926) - vitamin D levels)
FADS1 (rs174546 (http://www.snpedia.com/index.php/Rs174546)- LDL cholesterol levels)
EDAR (rs3827760 (http://www.snpedia.com/index.php/Rs3827760) - hair thickness)
TLR6 (rs7661887 - immune system)

All of them are tested by 23andMe and some by FTDNA's Family Finder too.

This graph shows the evolution of the various alleles.

http://www.eupedia.com/images/Mathieson-2015-graph.png


The alleles for fair skin are in blue and green. Mesolithic Europeans had dark skin (only a few samples derived for SLC24A5). Neolithic farmers were usually derived for SLC24A5, while Steppe people were derived for both SLC24A5 and SLC45A2.

Blue eyes were very common among Mesolithic Europeans, while Neolithic farmers and Yamna people had mixed eye colours.

Lactase persistence only starting taking off in the Chalcolithic, but underwent a very strong positive selection since then.

Lipid levels constantly increased over time, as if food became progressively scarcer as the population grew.

The gene for vitamin D production has oscillated over time, but it looks like the recent selection has been against increased vitamin D production, probably because people got their vit. D from milk and drank more milk as they became lactose tolerant.

Fire Haired14
15-03-15, 10:56
Don't mean to come off as arrogant Maciamo. I just want to let you know that Geneticker tested the Haak genomes for many pigmentation SNPs, which revealed alot of new info. Here's a link to his analysis (http://genetiker.wordpress.com/2015/03/07/phenotype-snps-from-prehistoric-europe/) and below are two threads I made about them. The most surprising result to me is that Mesolithic Swedes and Russians had markers for light skin along with every hair color, which didn't seem possible because of results from Mesolithic west Europe.

Red hair existed in pre-historic Europe (http://www.eupedia.com/forum/threads/30952-Red-hair-existed-in-pre-historic-Europe)
Mesolithic source of Pale pigmentation in modern Europe? (http://www.eupedia.com/forum/threads/30957-Mesolithic-source-of-Pale-pigmentation-in-modern-Europe)


The alleles for fair skin are in blue and green. Mesolithic Europeans had dark skin. Neolithic farmers brought one of the two alleles (SLC24A5), while Steppe people brought both alleles.

Most Mesolithic Swedes and the two Mesolithic Russians had a derived alleles in rs1426654 and Rs16891982. The vast majority but not all Neolithic farmers have two derived alleles in rs1426654, and very few have 1 or 2 derived alleles in rs16891982. All Yamna samples have two derived alleles in rs1426654, and only a few have a derived allele in rs16891982(consistent with Wilde. 2014).

Most Bronze age samples from central Europe and Siberia(Andronovo, etc.) have a derived allele in rs16891982. Although not at modern frequencies.


Blue eyes were very common among Mesolithic Europeans, but not Neolithic farmers. Yamna people had mixed eye colours.

12/13 Mesolithic Europeans have GG in Rs12913832. The only one that doesn't is Karelia_HG who had AA. 50% of LBK_EN have GG in rs12913832, a good amount of Neolithic Hungarians did, and Gok2 a Neolithic Swede did. Alot of EEF would have had blue eyes, except maybe in Spain were almost all samples have AA. Yamna was much darker eyed(~90%) than Neolithic central Europeans.

All Bell beaker and Corded ware individuals tested have at least one A allele in that SNP. I'm pretty sure all the Late Neolithic Germans actually had an A allele. Most Unetice samples have GG and the Urnfield guy had GG.

Maciamo
15-03-15, 11:24
Don't mean to come off as arrogant Maciamo. I just want to let you know that Geneticker tested the Haak genomes for many pigmentation SNPs, which revealed alot of new info. Here's a link to his analysis (http://genetiker.wordpress.com/2015/03/07/phenotype-snps-from-prehistoric-europe/) and below are two threads I made about them. The most surprising result to me is that Mesolithic Swedes and Russians had markers for light skin along with every hair color, which didn't seem possible because of results from Mesolithic west Europe.

Red hair existed in pre-historic Europe (http://www.eupedia.com/forum/threads/30952-Red-hair-existed-in-pre-historic-Europe)
Mesolithic source of Pale pigmentation in modern Europe? (http://www.eupedia.com/forum/threads/30957-Mesolithic-source-of-Pale-pigmentation-in-modern-Europe)



Most Mesolithic Swedes and the two Mesolithic Russians had a derived alleles in rs1426654 and Rs16891982. The vast majority but not all Neolithic farmers have two derived alleles in rs1426654, and very few have 1 or 2 derived alleles in rs16891982. All Yamna samples have two derived alleles in rs1426654, and only a few have a derived allele in rs16891982(consistent with Wilde. 2014).

Most Bronze age samples from central Europe and Siberia(Andronovo, etc.) have a derived allele in rs16891982. Although not at modern frequencies.



12/13 Mesolithic Europeans have GG in Rs12913832. The only one that doesn't is Karelia_HG who had AA. 50% of LBK_EN have GG in rs12913832, a good amount of Neolithic Hungarians did, and Gok2 a Neolithic Swede did. Alot of EEF would have had blue eyes, except maybe in Spain were almost all samples have AA. Yamna was much darker eyed(~90%) than Neolithic central Europeans.

All Bell beaker and Corded ware individuals tested have at least one A allele in that SNP. I'm pretty sure all the Late Neolithic Germans actually had an A allele. Most Unetice samples have GG and the Urnfield guy had GG.

Thanks for the extra details. I was just explaining the graph from this paper though.

Sile
15-03-15, 11:26
@fire

So 50% of LBK_EN ..................you know there are 12 samples of LBK_EN from Germany alone.................I counted 9 of the 12 had blue or green eyes

Angela
15-03-15, 21:50
The results for the depigmentation snps mirror those found in Genetiker's analysis.

Not to belabor the point, but Yamnaya Indo-Europeans were not significantly derived for SLC42A5, and did not possess significant levels of the "blue-eyed" gene. So, it's highly unlikely that this particular group, the Samara Indo-Europeans, brought depigmentation genes to Europe. We'll have to see what surprises the results of other groups in the Horizon might hold for us.

The authors do not opine to any great degree about the source of these snps, which is understandable given Patterson's recent comment on another blog about how the "source" of certain mutations may be very difficult to ascertain, given that it may no longer even exist in the areas where it arose.

They do say, however, that:
7143


I agree with what I think is their conclusion about SLC24A5, that it might very well have existed in the farmers even before they got to Europe, which would tie in very nicely with the results of the studies which showed a starburst radiation out of the Caucasus. SLC42A5 is more problematic. In the excerpt above, they mention that SLC42A5 was present in the Early Neolithic, but from another part of the paper it is clear that it also existed near contemporaneously with the SHG. I don't know of any likely migration path from SHG to early Neolithic farmers or vice versa, so perhaps it arose in some more eastern group (given the western hunter-gatherers had so few depigmentation alleles of any kind) in a place which could feed into both populations? I remember doing some research on the Motala group at one point, and discovering that they were new to the area. I must have stupidly tagged it incorrectly, because I can't find it in my files. Does anyone know anything about that? I also wonder if it's associated with more "ANE" type populations?

In connection to Motala, it's very interesting indeed that 4/7 Motala samples are derived for the Asian EDAR mutations, which according to the authors indicates "gene flow between the ancestors of the Scandinavian Hunter-Gatherers and the Han."

Having said all that, the focus of the paper seems to me to be not on the source for any of the snps, but on the very recent selection that has gone on in evolutionary terms around a very small number of snps. I think that the authors tried to point out that their analysis shows these changes aren't all because of different migration patterns.

Lactase persistence shows the strongest markers of selection, and it wasn't present in the Yamnaya or the EHG or the SHG or the WHG or the EEF. It first appears in a Bell Beaker sample. I wonder, given the "western" cast of Bell Beaker, if it has something to do with Atlantic Europe? Surprising that despite the fact that they practiced pastoralism, the Yamnaya Indo-Europeans didn't have it, and neither did the EHG. Maybe it might show up in other Indo-European groups? I tend to doubt it, on balance, because this group has lots of samples from the Yamnaya horizon, and I don't think they would have worded this paper in the way they did if it is present on the steppe, but who knows?

Also very interesting that the derived FADSI snp for decreased trigliceride levels was under selection in the Neolithic...very important if you're eating a high starch diet. Likewise, that in central European LN/Early Bronze there begins to be some selection for higher BMI levels, a selection present in CEU, which could stand for British Isles/North Sea, I think. (A Mormon who used to post on 23andm enlightened all of us about the conversions in Denmark etc and how that impacted Mormon genetics.)

Any ideas from anybody why higher body fat percentages compared to lean muscle mass would suddenly be more advantageous at that time and in that environment? Or am I misunderstanding something?

I also wonder how the selection for shorter height that shows up in the Iberian Neolithic factors into all of this.

The mutations involved with circulating Vitamin D are the ones who have the most up and down movement. Any ideas? I don't think it could have been that they didn't need them because they were drinking more milk, because there isn't much Vitamin D in milk, is there? That's why it has to be fortified?

Another interesting selection pattern is the de-selection for blue eyes that the authors maintain has been going on in southern Europe. (and other places no doubt) It must have something to do with annual UV radiation levels or something, yes? I have no idea what makes blue eyes so particularly disadvantageous in more southerly climates. Certainly, a lot of southern Europeans are homozygous for both skin depigmentation alleles. Does anyone know of any good research on this?

LeBrok
15-03-15, 22:30
HERC2 (rs12913832 (http://www.snpedia.com/index.php/Rs12913832) - eye color)
SLC24A5 (rs1426654 (http://www.snpedia.com/index.php/Rs1426654) - skin pigmentation)
SLC45A2 (rs16891982 (http://www.snpedia.com/index.php/Rs16891982)- skin pigmentation)
LCT (rs4988235 (http://www.snpedia.com/index.php/Rs4988235)- lactase peristence)
NADSYN1 (rs7940244 (http://www.snpedia.com/index.php/Rs7944926) - vitamin D levels)
FADS1 (rs174546 (http://www.snpedia.com/index.php/Rs174546)- LDL cholesterol levels)
EDAR (rs3827760 (http://www.snpedia.com/index.php/Rs3827760) - hair thickness)
TLR6 (rs7661887 - immune system)

http://www.eupedia.com/images/Mathieson-2015-graph.png
Thanks for short explanation. I can't find enough time these days to read whole papers.




Lipid levels constantly increased over time, as if food became progressively scarcer as the population grew. This could be tricky to explain. Lipids are involved in many mechanisms in our body from cell membrane, anti inflammatory function, to energy production. LDL by itself is not that bad and obviously plays a positive role in our bodies. The important is ratio between LDL and HDL to keep people healthy. The imbalance between these 2 causes maladies.


The gene for vitamin D production has oscillated over time, but it looks like the recent selection has been against increased vitamin D production, probably because people got their vit. D from milk and drank more milk as they became lactose tolerant. European population got lighter with time, so perhaps NADSYN1 is not that important now and evolution doesn't care to select it anymore.

Maciamo
16-03-15, 11:39
The results for the depigmentation snps mirror those found in Genetiker's analysis.

Not to belabor the point, but Yamnaya Indo-Europeans were not significantly derived for SLC42A5, and did not possess significant levels of the "blue-eyed" gene. So, it's highly unlikely that this particular group, the Samara Indo-Europeans, brought depigmentation genes to Europe. We'll have to see what surprises the results of other groups in the Horizon might hold for us.

I admit that I only browsed quickly (10 minutes) through the paper before posting the summary above. I didn't have time to read Genetiker's analysis yet.



Lactase persistence shows the strongest markers of selection, and it wasn't present in the Yamnaya or the EHG or the SHG or the WHG or the EEF. It first appears in a Bell Beaker sample. I wonder, given the "western" cast of Bell Beaker, if it has something to do with Atlantic Europe? Surprising that despite the fact that they practiced pastoralism, the Yamnaya Indo-Europeans didn't have it, and neither did the EHG. Maybe it might show up in other Indo-European groups? I tend to doubt it, on balance, because this group has lots of samples from the Yamnaya horizon, and I don't think they would have worded this paper in the way they did if it is present on the steppe, but who knows?

I really don't see why lactase persistence would have been positively selected in a society like that of the Megalithic people. As for Atlantic people bringing genes to Central Europe, I have said for a while that the Bell Beaker was not a group of people, but just a trade network. The people who lived during the Bell Beaker period in Germany were in all likelihood descended mostly from LBK-related cultures, not new migrants from Iberia or other parts of Atlantic Europe. The new genes came the PIE Steppe people whose R1b-M269 lineage was identified in the few BB samples tested. These people were clearly first or second generation hybrids of two distinct populations: Neolithic Germans (descended from LBK, Rössen, etc.), and the newly arrived Yamna descendants.

It is more logical that the LP allele was positively selected among people who were almost exclusively cattle pastoralists like Yamna people, then cereal farmers of Neolithic Europe. It is true that the Funnelbeaker people of Germany and Scandinavia also raised cattle (as well as sheep, pigs and goats), but selection pressures for digesting lactose would have been much weaker than in the steppe, where cereals weren't a main source of sugar.

What we can say with certainty is that today lactase persistence is present mostly among western Europeans and Scandinavians (all R1b countries), with the highest percentages observed in the British Isles, the Netherlands, Denmark and southern Sweden. The fact that the Irish and the Scots have similarly high percentages as Scandinavians, and higher than the Germans, suggests that the lactase persistence allele really was spread by R1b people, and not by the Neolithic population of Germany or Scandinavia.

It is possible that the mutation arose somewhere in Central Europe and was "picked up" by R1b tribes on their way to the British Isles. It did not necessarily enter the R1b population in the western steppe.Looking at the distribution map of the 13910*T allele (figure (b) below) associated with LP in Europeans, it is amazing to see just how closely it mirrors the distribution of R1b lineages, and not just R1b-M269, but even R1b-V88 in Africa (Maghreb, northern Cameroon). Note especially the distrbution of the 13910*T allele in Eastern Europe, Central Asia and India, which, just like R1b, is present but at low frequency. West Africans, East Africans, Arabs and Mongols all have different mutations conferring LP. If the 13910*T allele had arisen in Mesolithic or Neolithic Europeans, it wouldn't be found in northern Cameroon or India today. If it had originated in the Near East, it would still be found there. The only light blue dot on the map is in northern Mesopotamia, close to where I think cattle were domesticated by R1b people.


http://d1vn86fw4xmcz1.cloudfront.net/content/366/1566/863/F1.medium.gif



Also very interesting that the derived FADSI snp for decreased trigliceride levels was under selection in the Neolithic...very important if you're eating a high starch diet. Likewise, that in central European LN/Early Bronze there begins to be some selection for higher BMI levels, a selection present in CEU, which could stand for British Isles/North Sea, I think. (A Mormon who used to post on 23andm enlightened all of us about the conversions in Denmark etc and how that impacted Mormon genetics.)

Any ideas from anybody why higher body fat percentages compared to lean muscle mass would suddenly be more advantageous at that time and in that environment? Or am I misunderstanding something?


Too low levels of LDL cholesterol have been associated with increased anxiety and depression. Perhaps those alleles were just selected for the positive psychological benefits associated with higher cholesterol. Ancient people didn't know that cholesterol was bad for the heart. They didn't even know what was cholesterol was. What happened is that the more joyful people had more children, even if that meant a selection for higher cholesterol levels.




The mutations involved with circulating Vitamin D are the ones who have the most up and down movement. Any ideas? I don't think it could have been that they didn't need them because they were drinking more milk, because there isn't much Vitamin D in milk, is there? That's why it has to be fortified?


The common foods with the highest vitamin D contents (http://www.healthaliciousness.com/articles/high-vitamin-D-foods.php) are oily fish, dairy products, pork and eggs. German and Scandinavian HG ate a lot of fish. Yamna people were probably the first to consume large quantities of dairy products. Neolithic Europeans ate pork. Chickens and eggs only came later, during the Iron Age. As all these came together and formed a more diversified and nutritional diet, the need for vitamin D decreased. I think that it is especially since the Middle Ages that Europeans started to consume cheese, butter, milk, eggs and their derivatives (crêpes/pancakes, waffles, cakes) on a regular basis.

Another factor was the increasing selection for fairer skin, as demonstrated by the sharp rise in SLC45A2 derive alleles since the Bronze Age, and surely also for MC1R mutations for red hair, freckles and very pale skin in Northwest Europe.


Another interesting selection pattern is the de-selection for blue eyes that the authors maintain has been going on in southern Europe. (and other places no doubt) It must have something to do with annual UV radiation levels or something, yes? I have no idea what makes blue eyes so particularly disadvantageous in more southerly climates. Certainly, a lot of southern Europeans are homozygous for both skin depigmentation alleles. Does anyone know of any good research on this?

I have noticed among my relatives and friends that people with blue eyes (like me) are more sensitive to strong sunlight, but see better in the dark. I have noticed when I lived in Japan that Japanese people, who don't have any allele for blue eyes, see considerably less well in the dark than I do. On the other hand every time I go out in strong sunlight my eyes cry from the irritation.

I can't easily imagine why blue eyed people would have less children in hot countries (it doesn't affect their survival or fertility), but it makes sense that darker eyes are better suited to strong sunlight (just like for hair and skin).

giuseppe rossi
16-03-15, 14:21
Frequencies of HERC2 (rs12913832 (http://www.snpedia.com/index.php/Rs12913832) - eye color) among Europeans

Frequencies of Allele G for blue eyes.

Whites from Utah: 77%
Brits: 82%
Finns: 91%
North Italians from Verona: 53%
Tuscans: 42%
Spaniards: 32%

Source: ALFRED alleles and 1000genomes.

Expredel
16-03-15, 14:22
What we can say with certainty is that today lactase persistence is present mostly among western Europeans and Scandinavians (all R1b countries), with the highest percentages observed in the British Isles, the Netherlands, Denmark and southern Sweden. The fact that the Irish and the Scots have similarly high percentages as Scandinavians, and higher than the Germans, suggests that the lactase persistence allele really was spread by R1b people, and not by the Neolithic population of Germany or Scandinavia.

It is possible that the mutation arose somewhere in Central Europe and was "picked up" by R1b tribes on their way to the British Isles. It did not necessarily enter the R1b population in the western steppe.Looking at the distribution map of the 13910*T allele (figure (b) below) associated with LP in Europeans, it is amazing to see just how closely it mirrors the distribution of R1b lineages, and not just R1b-M269, but even R1b-V88 in Africa (Maghreb, northern Cameroon). Note especially the distrbution of the 13910*T allele in Eastern Europe, Central Asia and India, which, just like R1b, is present but at low frequency. West Africans, East Africans, Arabs and Mongols all have different mutations conferring LP. If the 13910*T allele had arisen in Mesolithic or Neolithic Europeans, it wouldn't be found in northern Cameroon or India today. If it had originated in the Near East, it would still be found there. The only light blue dot on the map is in northern Mesopotamia, close to where I think cattle were domesticated by R1b people.


http://d1vn86fw4xmcz1.cloudfront.net/content/366/1566/863/F1.medium.gif


If lactose persistence arose in R1b we would find it in Spain, and the R1b V88 distribution in Africa doesn't match the lactose persistence distribution in Africa.

The best explanation is lactose persistence spreading with Germanic migrations and their milk drinking culture around 500 BC. Milk consumption is highest in Sweden. This seems really rather obvious.

Maciamo
16-03-15, 14:45
If lactose persistence arose in R1b we would find it in Spain, and the R1b V88 distribution in Africa doesn't match the lactose persistence distribution in Africa.

The best explanation is lactose persistence spreading with Germanic migrations and their milk drinking culture around 500 BC. Milk consumption is highest in Sweden. This seems really rather obvious.

Not necessarily. R1b-V88 in Spain travelled a very long way through Africa. It is Middle Neolithic. As the autosomal data shows the Spanish R1b-V88 sample has been thoroughly admixed with other Neolithic populations, so that hardly any of the original autosomal DNA remained. Therefore it's not surprising that this single mutation was lost along the way. In fact it would be utterly surprising if it was still there at all.

giuseppe rossi
16-03-15, 15:32
According to this website, Sardinians are the Europeans with the lowest level of lactose persistence.

http://www.ucl.ac.uk/mace-lab/resources/glad

Maciamo
16-03-15, 18:07
According to this website, Sardinians are the Europeans with the lowest level of lactose persistence.

http://www.ucl.ac.uk/mace-lab/resources/glad

They also have the lowest level of Indo-European autosomal DNA (virtually no Gedrosian or East European). That makes perfect sense if the LP allele was spread by teh Indo-Europeans.

giuseppe rossi
16-03-15, 18:43
Lactase persistance in Southern Europe.

Only regionalized data.

Greek Cretan: 44%
Continental Greek: 55%
Neapolitan: 46%
North Italian: 49%
Sardinian: 14%
Sicilian: 29%
Greek Cypriot: 34%
Galician: 66%

It looks like there is a correlation with both Indo European and especially Celto Germanic ancestry.

giuseppe rossi
16-03-15, 18:58
They also have the lowest level of Indo-European autosomal DNA (virtually no Gedrosian or East European). That makes perfect sense if the LP allele was spread by teh Indo-Europeans.

Lactase persistance first apparead in the Bell Beaker culture 4300 years BP.

Euclidean distance in Bell Beaker.

S Dutch 7.3315543
French 7.4857465
SWEnglish 8.9121658
SEEnglish 10.143397
WGerman 11.279248



S Dutch 14.150768
French 15.658902
Hinxton4 15.728522
NGerman 16.217733
SWEnglish 16.906883



S Dutch 8.9668085
NGerman 11.094324
SWEnglish 11.309889
French 11.593037
WGerman 12.447302


-----------------------------------------------------------


Icelandic 6.1312678
Danish 6.5065283
SWEnglish 7.0875454
SEEnglish 7.206171
N Dutch 7.4365277



Hinxton4 10.710051
NGerman 10.858956
N Dutch 11.577781
Danish 11.739996
Irish 11.760162




Danish 10.41551
Icelandic 10.640087
NGerman 11.053448
N Dutch 11.232878
W Nor 11.378201



NGerman 8.7288958
Danish 10.808824
N Dutch 11.56526
S Dutch 11.621216
WGerman 12.408666

Expredel
17-03-15, 04:35
Not necessarily. R1b-V88 in Spain travelled a very long way through Africa. It is Middle Neolithic. As the autosomal data shows the Spanish R1b-V88 sample has been thoroughly admixed with other Neolithic populations, so that hardly any of the original autosomal DNA remained. Therefore it's not surprising that this single mutation was lost along the way. In fact it would be utterly surprising if it was still there at all.
Well, R1b-V88 in Africa matches properly when looking at different maps of lactose persistence. So we may just need better maps. Fairly obvious that the trait must have been rare among early Celts.

Looking at different maps I see a solid connection with R1a assuming LP in India finds its origin there.

Scandinavia is definitely the location where selection for the trait was the strongest.

Maciamo
17-03-15, 08:45
Well, R1b-V88 in Africa matches properly when looking at different maps of lactose persistence. So we may just need better maps. Fairly obvious that the trait must have been rare among early Celts.

Looking at different maps I see a solid connection with R1a assuming LP in India finds its origin there.

Scandinavia is definitely the location where selection for the trait was the strongest.

Granted, the LP allele had a low frequency during the Neolithic and Early Bronze Age, which is why most Yamna samples are negative (all those tested to date, but I surely expect others will be derived for LP), and also why African R1b populations have very low LP frequencies. The strong positive selected for the LP allele must have taken place progressively in the last 4000 years in Europe. The fact that Iberians have considerably lower LP frequencies than northern Europeans suggests that the LP selection was not yet half way in the first millennium BCE (Hallstatt period) when Celts migrated in large number to Iberia. I don't expect that frequencies above 80% were achieved in northern Europe before the late Middle Ages.

giuseppe rossi
17-03-15, 09:54
Frequencies of SLC45A2 (rs16891982 (http://www.snpedia.com/index.php/Rs16891982)- skin pigmentation) among Europeans

Frequencies of Allele G for light skin.

Whites from Utah: 98%
Brits: 98%
Finns: 96%
North Italians from Verona: 94%
Tuscans: 97%
Spaniards: 82%

Source: ALFRED alleles and 1000genomes.

giuseppe rossi
17-03-15, 10:34
Granted, the LP allele had a low frequency during the Neolithic and Early Bronze Age, which is why most Yamna samples are negative (all those tested to date, but I surely expect others will be derived for LP), and also why African R1b populations have very low LP frequencies. The strong positive selected for the LP allele must have taken place progressively in the last 4000 years in Europe. The fact that Iberians have considerably lower LP frequencies than northern Europeans suggests that the LP selection was not yet half way in the first millennium BCE (Hallstatt period) when Celts migrated in large number to Iberia. I don't expect that frequencies above 80% were achieved in northern Europe before the late Middle Ages.

It's more likely that R1b-DF27 arrived in Iberia from Italy, rather than from Central Europe.

The highest diversity of R1b-P312 is in Italy.

http://r1b.org/imgs/Early_R1b_Copper_Age_Migrations_v02.png

Didn't they find Tuscan like farmers in Iberia lately?

It looks like modern Iberians are mostly a mix of Sardinian/Tuscan like neolitich/copper age farmers and local Mesolitich hunther gatherers, who had already elevated levels of ANE admixture.

Maciamo
17-03-15, 11:32
It's more likely that R1b-DF27 arrived in Iberia from Italy, rather than from Central Europe.

The highest diversity of R1b-P312 is in Italy.

http://r1b.org/imgs/Early_R1b_Copper_Age_Migrations_v02.png

Didn't they find Tuscan like farmers in Iberia lately?

It looks like modern Iberians are mostly a mix of Sardinian/Tuscan like neolitich/copper age farmers and local Mesolitich hunther gatherers, who had already elevated levels of ANE admixture.

Keep in mind that there is very little genetic data from France at the moment. I wouldn't be surprised if P312 had a higher genetic diversity in France. The Alps are difficult to cross, so P312 more likely went straight from Germany to France (no natural border except the Rhine).

giuseppe rossi
17-03-15, 12:12
Keep in mind that there is very little genetic data from France at the moment. I wouldn't be surprised if P312 had a higher genetic diversity in France. The Alps are difficult to cross, so P312 more likely went straight from Germany to France (no natural border except the Rhine).

Lame excuse.

There are more French samples aviable than Italian ones.

Look how the map shows that L21 and DF27 have the highest diversity in France, and both came from the Italian P312.

Pax Augusta
17-03-15, 14:30
The Alps are difficult to cross

Not anywhere. There are many passages: one between France and Italy near the coast (Provence/Cote d'Azur and Liguria). Others between Italy and Switzerland (Piedmont, Lombardy and Canton Ticino), Italy and Austria (Trentino-Alto Adige, Veneto, Friuli and Styria, Tyrol, Carinthia) and Italy and former Yugoslavia.

Drac II
18-03-15, 06:50
Frequencies of SLC45A2 (rs16891982 (http://www.snpedia.com/index.php/Rs16891982)- skin pigmentation) among Europeans

Frequencies of Allele G for light skin.

Norwegians: 98%
Poles: 98%
Finns: 96%
North Italians from Verona: 94%
Spaniards from Madrid: 92%
Greeks from Thessaloniki: 86%
Spaniards from all over Spain (including islanders): 82%
Germans from Lower Saxony (which ironically is in reality one of the lightest areas of Germany): 66%

Source: ALFRED alleles and 1000genomes.

Sile
18-03-15, 07:53
The complere indo-european language tree in this article ...................used by Haak and Co.

http://www.theleadsouthaustralia.com.au/industries/research-development/ancient-skeletons-hold-the-key-to-origins-of-the-spread-of-indoeuropean-language/


since Anatolian is the first and Albanian is the second, then clearly Albanian originated somewhere in or near anatolia ............my opinion
(http://www.theleadsouthaustralia.com.au/industries/research-development/ancient-skeletons-hold-the-key-to-origins-of-the-spread-of-indoeuropean-language/)

bicicleur
18-03-15, 09:53
It's more likely that R1b-DF27 arrived in Iberia from Italy, rather than from Central Europe.

The highest diversity of R1b-P312 is in Italy.

http://r1b.org/imgs/Early_R1b_Copper_Age_Migrations_v02.png

Didn't they find Tuscan like farmers in Iberia lately?

It looks like modern Iberians are mostly a mix of Sardinian/Tuscan like neolitich/copper age farmers and local Mesolitich hunther gatherers, who had already elevated levels of ANE admixture.

2200 BC the tin mines in Cornwall were under controll of Wessex culture (Bell Beaker), a broadskulled invading elite group that married local women, and their skulls gradually became narrower
+/- 1000 BC the broadskulled Goidels invaded the British Isles and took over power
so I suspect L21 arrived on the British Isles not earlier than +/- 1000 BC

giuseppe rossi
18-03-15, 10:39
2200 BC the tin mines in Cornwall were under controll of Wessex culture (Bell Beaker), a broadskulled invading elite group that married local women, and their skulls gradually became narrower
+/- 1000 BC the broadskulled Goidels invaded the British Isles and took over power
so I suspect L21 arrived on the British Isles not earlier than +/- 1000 BC

We can't know for sure until more ancient DNA from the isles is aviable.

Angela
18-03-15, 20:03
If lactose persistence arose in R1b we would find it in Spain, and the R1b V88 distribution in Africa doesn't match the lactose persistence distribution in Africa.

The best explanation is lactose persistence spreading with Germanic migrations and their milk drinking culture around 500 BC. Milk consumption is highest in Sweden. This seems really rather obvious.

There was a recent study about lactase persistence in Africa which is very informative:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3980415/

Lactase persistence in Africa derives from five separate mutations, only one of which is the European variant, or 13910T. The authors maintain that three of the others spread from the general area of the Levant/Arabia and one arose in East Africa. They have high frequency in pastoralist societies. So, there is nothing uniquely "European" about mutations for Lactase Persisence or selection for them in such societies.

In western Africa, the Hausa, a Chadic speaking equestrian based society of pastoralists, who consume a lot of milk products, including fresh milk, have levels of 20-40% R1b, but all of it is V88, for which a steppe origin and Indo-European connection has never, to my knowledge, been posited. It may be true that they were pastoralists even in the Levant or Anatolia, but would they necessarily be the only haplogroup in Anatolia that kept cattle? Anyway, the frequency of 13910T in them is either 13.90 or 22.92 percent. They also show a frequency of 11.55% of the 14010 derived allele for Lactase Persistence.

The Fulani, also pastoralists who incorporate milk products into their diet, but in their case Niger Congo speaking, have a frequency of 14.3% for R1b V-88, but a frequency of the European 13910T variant of from 11 to 39% depending on the area and the study. They also have from 12 to 14% frequency of the 14010 Lactase Persistence variant.

On the other hand, the Oudelme of Cameroon are 95% V88 but in the one test done for the presence of lactase persistence alleles, their score was 0. Now, that seems a little odd to me, so perhaps they have some, but anyone who wants to draw any conclusive correlation between the presence specifically of R1b V88 and the "European" variant of a Lactase Persistence mutation is going to have to do more research.

Oh, and the drawing of a correlation is made more difficult by the data on North Africans. The "European" Lactase Persistence variant has frequencies in Mozabite Berbers of 22,7% and in general Algerians of 33.3%, depending on the study. Their level of R1b is, from a quick search, only about 3%, all of it V-88. There's no data for other areas.

Expredel
18-03-15, 22:48
This link might be of interest as to African and European r1b.

http://bellbeakerblogger.blogspot.com/2014/10/african-origin-of-bell-beaker-lithics_30.html?utm_source=BP_featured

Sile
07-04-15, 08:37
Another supplementary paper from the Haak paper ................nice maps as well

http://rspb.royalsocietypublishing.org/content/royprsb/suppl/2015/03/20/rspb.2015.0339.DC1/rspb20150339supp1.pdf

Fire Haired14
07-04-15, 09:01
Another supplementary paper from the Haak paper ................nice maps as well

http://rspb.royalsocietypublishing.org/content/royprsb/suppl/2015/03/20/rspb.2015.0339.DC1/rspb20150339supp1.pdf

This isn't Haak 2015.

Sile
07-04-15, 11:41
This isn't Haak 2015.

what is this then, his brother ..the other haak

from Haak 2005 paper
Ancient DNA from the First European Farmers in 7500-Year-Old Neolithic Sites
to

http://www.biomedcentral.com/1471-2148/10/304#B3

to

Brotherton 2013 paper on H mtdna

to

laz paper

to

Haak 2015 paper

to this I posted above , are all connected, they slowly have been working on them and will continue to work on them.

Sile
27-04-15, 08:54
2 years ago, this paper ( below )
Ancient Europeans Mysteriously Vanished 4,500 Years Ago
by Tia Ghose, Staff Writer | April 23, 2013 11:09am ET
skeleton excavated from a grave in Sweden
DNA taken from ancient European skeletons reveals that the genetic makeup of Europe mysteriously transformed about 4,500 years ago, new research suggests. Here, a skeleton, not used in the study, but from the same time period, that was excavated from a grave in Sweden.
The genetic lineage of Europe mysteriously transformed about 4,500 years ago, new research suggests.
The findings, detailed today (April 23) in the journal Nature Communications, were drawn from several skeletons unearthed in central Europe that were up to 7,500 years old.
"What is intriguing is that the genetic markers of this first pan-European culture, which was clearly very successful, were then suddenly replaced around 4,500 years ago, and we don't know why," said study co-author Alan Cooper, of the University of Adelaide Australian Center for Ancient DNA, in a statement. "Something major happened, and the hunt is now on to find out what that was."
The new study also confirms that people sweeping out from Turkey colonized Europe, likely as a part of the agricultural revolution, reaching Germany about 7,500 years ago.
For decades, researchers have wondered whether people, or just ideas, spread from the Middle East during the agricultural revolution that occurred after the Mesolithic period.
To find out, Cooper and his colleagues analyzed mitochondrial DNA, which resides in the cells' energy-making structures and is passed on through the maternal line, from 37 skeletal remains from Germany and two from Italy; the skeletons belonged to humans who lived in several different cultures that flourished between 7,500 and 2,500 years ago. The team looked a DNA specifically from a certain genetic group, called haplogroup h, which is found widely throughout Europe but is less common in East and Central Asia.
The researchers found that the earliest farmers in Germany were closely related to Near Eastern and Anatolian people, suggesting that the agricultural revolution did indeed bring migrations of people into Europe who replaced early hunter-gatherers.
But that initial influx isn't a major part of Europe's genetic heritage today.
Instead, about 5,000 to 4,000 years ago, the genetic profile changes radically, suggesting that some mysterious event led to a huge turnover in the population that made up Europe.

which continued until the Haak paper of 2015.
With both papers and everything in between indicating that people and markers from pre 4500BC do not match markers from post 4500BC to today , why do we pursue this nonsense of motala, oetzi etc.
Clearly the Neolithic markers found in central germany by Haak and all others markers are the original europeans and do not match anything from Gamba and the hungarian or yamnya finds.

All I see is that any markers belonging to the group K-526 ( which is ydna Q, R, M , S ) are the first "barbarian invaders" of Europe.

Do we have a list of markers from older than 4500BC somewhere?

Arame
27-04-15, 11:04
Sile


Instead, about 5,000 to 4,000 years ago, the genetic profile changes radically, suggesting that some mysterious event led to a huge turnover in the population that made up Europe.

Well something important also happened in Armenia at this period. The population turnover was not as huge as elsewhere because mountains helped the ancient population to survive. But we see a clear change in archaeology (except some mountains regions ). This period was the decline of Kur-Arax culture.

arvistro
27-04-15, 13:07
The complere indo-european language tree in this article ...................used by Haak and Co.
http://www.theleadsouthaustralia.com.au/industries/research-development/ancient-skeletons-hold-the-key-to-origins-of-the-spread-of-indoeuropean-language/


since Anatolian is the first and Albanian is the second, then clearly Albanian originated somewhere in or near anatolia ............my opinion
(http://www.theleadsouthaustralia.com.au/industries/research-development/ancient-skeletons-hold-the-key-to-origins-of-the-spread-of-indoeuropean-language/)
Strange language tree. That is if it is supposed to show which language branched off after which.

Italic and Celtic branching off separately. Armenian branching AFTER Italic/Celtic, BEFORE Germanic.
Tocharian branching of from Tocharo-Balto-Slavic after Germanic.

And Balto-Slavic just sitting there till the end. Also what I find strange, maybe just because of me not being pro is that Indo-Iranian is so many language groups away from Balto-Slavic. Although maybe it is just because I always compared Sanscrit to Lithuanian, and in all articles those are compared. But Sanscrit is no more a language. If we compared modern Indo-Iranian languages they might have been miles away. Further than say Germanic.

Ok, maybe off topic here, since this is linguistics thing :)