Phenotype SNPs from Ice Age Europe

Below are derived allele counts and total numbers of reads for SNPs that have a large effect on phenotype for 37 genomes from Ice Age Europe. Nonzero derived allele counts are in bold. Note that small derived allele counts may be due to DNA damage.

Some of my previous phenotype SNP posts are here:

ASIP, rs2424984, Veddoid brown skin

Sample        Country  Years BP       Culture        D/T
Goyet Q116-1  Belgium  35,160–34,430  Aurignacian    0/1
Villabruna    Italy    14,180–13,780  Epigravettian  1/1

ASIP, rs6058017, Veddoid brown skin

Sample           Country  Years BP       Culture      D/T
Afontova Gora 3  Russia   16,930–16,490  Unassigned   1/1
Goyet Q-2        Belgium  15,230–14,780  Magdalenian  1/1

EDAR, rs3827760, Mongoloid teeth, hair, etc.

Sample           Country  Years BP       Culture         D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian     0/10
Paglicci 133     Italy    34,580–31,210  Gravettian      0/1
Krems WA3        Austria  31,250–30,690  Gravettian      0/1
Věstonice 43     Czechia  30,710–29,310  Gravettian      0/1
Věstonice 16     Czechia  30,710–29,310  Gravettian      0/4
Goyet Q53-1      Belgium  28,230–27,720  Gravettian      0/1
Ostuni 1         Italy    27,810–27,430  Gravettian      0/2
El Mirón         Spain    18,830–18,610  Magdalenian     0/8
Afontova Gora 3  Russia   16,930–16,490  Unassigned      0/1
Goyet Q-2        Belgium  15,230–14,780  Magdalenian     0/1
Villabruna       Italy    14,180–13,780  Epigravettian   0/20
Iboussières 39   France   12,040–11,410  Epipaleolithic  0/1
Ranchot 88       France   10,240–9,930   Mesolithic      0/2
Berry-au-Bac     France   7,320–7,170    Mesolithic      0/1

IRF4, rs12203592, light hair and eyes, freckling

Sample           Country  Years BP       Culture         D/T
Muierii 2        Romania  33,760–32,840  Unassigned      0/1
Věstonice 43     Czechia  30,710–29,310  Gravettian      0/1
Věstonice 16     Czechia  30,710–29,310  Gravettian      0/3
Ostuni 1         Italy    27,810–27,430  Gravettian      0/3
El Mirón         Spain    18,830–18,610  Magdalenian     0/3
Afontova Gora 3  Russia   16,930–16,490  Unassigned      0/1
Villabruna       Italy    14,180–13,780  Epigravettian   10/10
Rochedane        France   13,090–12,830  Epipaleolithic  0/1

KITLG, rs12821256, blond hair

Sample         Country  Years BP       Culture         D/T
Goyet Q116-1   Belgium  35,160–34,430  Aurignacian     0/2
Pavlov 1       Czechia  31,110–29,410  Gravettian      0/1
Věstonice 16   Czechia  30,710–29,310  Gravettian      0/2
Ostuni 1       Italy    27,810–27,430  Gravettian      0/1
Hohle Fels 49  Germany  16,000–14,260  Magdalenian     0/1
Villabruna     Italy    14,180–13,780  Epigravettian   0/10
Rochedane      France   13,090–12,830  Epipaleolithic  0/1

KITLG, rs642742, Veddoid brown skin

Sample        Country  Years BP       Culture      D/T
Goyet Q116-1  Belgium  35,160–34,430  Aurignacian  1/1

MC1R, rs1110400, red hair

Sample           Country  Years BP       Culture         D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian     0/11
Věstonice 43     Czechia  30,710–29,310  Gravettian      0/2
Věstonice 16     Czechia  30,710–29,310  Gravettian      0/28
Ostuni 1         Italy    27,810–27,430  Gravettian      0/6
El Mirón         Spain    18,830–18,610  Magdalenian     0/31
Afontova Gora 3  Russia   16,930–16,490  Unassigned      0/2
Hohle Fels 79    Germany  15,070–14,270  Magdalenian     0/1
Villabruna       Italy    14,180–13,780  Epigravettian   0/33
Rochedane        France   13,090–12,830  Epipaleolithic  0/2
Falkenstein      Germany  9,410–8,990    Mesolithic      0/2
Bockstein        Germany  8,370–8,160    Mesolithic      0/1

MC1R, rs11547464, red hair

Sample        Country  Years BP       Culture         D/T
Goyet Q116-1  Belgium  35,160–34,430  Aurignacian     0/9
Muierii 2     Romania  33,760–32,840  Unassigned      0/1
Věstonice 13  Czechia  31,070–30,670  Gravettian      0/1
Pavlov 1      Czechia  31,110–29,410  Gravettian      0/1
Věstonice 43  Czechia  30,710–29,310  Gravettian      0/4
Věstonice 16  Czechia  30,710–29,310  Gravettian      0/12
Ostuni 1      Italy    27,810–27,430  Gravettian      0/3
Goyet Q56-16  Belgium  26,600–26,040  Gravettian      1/1
El Mirón      Spain    18,830–18,610  Magdalenian     1/20
Villabruna    Italy    14,180–13,780  Epigravettian   0/15
Rochedane     France   13,090–12,830  Epipaleolithic  0/1
Ranchot 88    France   10,240–9,930   Mesolithic      0/1
Falkenstein   Germany  9,410–8,990    Mesolithic      0/1

MC1R, rs1805005, blond hair, fair skin

Sample           Country  Years BP       Culture        D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian    0/2
Věstonice 16     Czechia  30,710–29,310  Gravettian     0/4
Ostuni 1         Italy    27,810–27,430  Gravettian     0/2
El Mirón         Spain    18,830–18,610  Magdalenian    0/3
Afontova Gora 3  Russia   16,930–16,490  Unassigned     0/3
Villabruna       Italy    14,180–13,780  Epigravettian  0/11
Ranchot 88       France   10,240–9,930   Mesolithic     0/1
Falkenstein      Germany  9,410–8,990    Mesolithic     0/1

MC1R, rs1805006, red hair, fair skin

Sample         Country  Years BP       Culture        D/T
Goyet Q116-1   Belgium  35,160–34,430  Aurignacian    0/3
Věstonice 13   Czechia  31,070–30,670  Gravettian     0/2
Věstonice 16   Czechia  30,710–29,310  Gravettian     0/10
Ostuni 1       Italy    27,810–27,430  Gravettian     0/1
El Mirón       Spain    18,830–18,610  Magdalenian    0/14
Hohle Fels 49  Germany  16,000–14,260  Magdalenian    0/2
Villabruna     Italy    14,180–13,780  Epigravettian  0/24
Ranchot 88     France   10,240–9,930   Mesolithic     0/2
Falkenstein    Germany  9,410–8,990    Mesolithic     0/1
Bockstein      Germany  8,370–8,160    Mesolithic     0/2
Berry-au-Bac   France   7,320–7,170    Mesolithic     0/1

MC1R, rs1805007, red hair, fair skin

Sample           Country  Years BP       Culture         D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian     0/11
Pavlov 1         Czechia  31,110–29,410  Gravettian      0/1
Věstonice 43     Czechia  30,710–29,310  Gravettian      1/5
Věstonice 16     Czechia  30,710–29,310  Gravettian      1/27
Ostuni 1         Italy    27,810–27,430  Gravettian      0/4
El Mirón         Spain    18,830–18,610  Magdalenian     0/33
Afontova Gora 3  Russia   16,930–16,490  Unassigned      0/1
Hohle Fels 79    Germany  15,070–14,270  Magdalenian     0/1
Villabruna       Italy    14,180–13,780  Epigravettian   2/32
Rochedane        France   13,090–12,830  Epipaleolithic  0/2
Falkenstein      Germany  9,410–8,990    Mesolithic      0/1

MC1R, rs1805008, red hair, fair skin

Sample           Country  Years BP       Culture         D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian     0/8
Věstonice 43     Czechia  30,710–29,310  Gravettian      0/2
Věstonice 16     Czechia  30,710–29,310  Gravettian      0/21
Ostuni 1         Italy    27,810–27,430  Gravettian      0/4
El Mirón         Spain    18,830–18,610  Magdalenian     0/17
Afontova Gora 3  Russia   16,930–16,490  Unassigned      0/2
Goyet Q-2        Belgium  15,230–14,780  Magdalenian     0/1
Villabruna       Italy    14,180–13,780  Epigravettian   2/25
Rochedane        France   13,090–12,830  Epipaleolithic  0/1
Falkenstein      Germany  9,410–8,990    Mesolithic      0/4
Bockstein        Germany  8,370–8,160    Mesolithic      0/1

MC1R, rs1805009, red hair, fair skin

Sample           Country  Years BP       Culture         D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian     0/9
Paglicci 133     Italy    34,580–31,210  Gravettian      0/1
Věstonice 13     Czechia  31,070–30,670  Gravettian      0/2
Věstonice 14     Czechia  31,070–30,670  Gravettian      0/1
Věstonice 43     Czechia  30,710–29,310  Gravettian      0/3
Věstonice 16     Czechia  30,710–29,310  Gravettian      0/27
Ostuni 1         Italy    27,810–27,430  Gravettian      0/5
El Mirón         Spain    18,830–18,610  Magdalenian     0/34
Afontova Gora 3  Russia   16,930–16,490  Unassigned      0/1
Hohle Fels 49    Germany  16,000–14,260  Magdalenian     0/1
Villabruna       Italy    14,180–13,780  Epigravettian   0/32
Rochedane        France   13,090–12,830  Epipaleolithic  0/1
Ranchot 88       France   10,240–9,930   Mesolithic      0/3

MCM6, rs182549, ability to digest milk

Sample        Country  Years BP       Culture        D/T
Goyet Q116-1  Belgium  35,160–34,430  Aurignacian    0/1
Věstonice 15  Czechia  31,070–30,670  Gravettian     1/1
El Mirón      Spain    18,830–18,610  Magdalenian    0/2
Villabruna    Italy    14,180–13,780  Epigravettian  0/1
Ranchot 88    France   10,240–9,930   Mesolithic     0/1
Bockstein     Germany  8,370–8,160    Mesolithic     0/1

MCM6, rs4988235, ability to digest milk

Sample           Country  Years BP       Culture         D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian     0/8
Věstonice 16     Czechia  30,710–29,310  Gravettian      0/13
Ostuni 2         Italy    29,310–28,640  Gravettian      0/1
Ostuni 1         Italy    27,810–27,430  Gravettian      0/1
El Mirón         Spain    18,830–18,610  Magdalenian     0/2
Afontova Gora 3  Russia   16,930–16,490  Unassigned      0/1
Burkhardtshöhle  Germany  15,080–14,150  Magdalenian     0/2
Villabruna       Italy    14,180–13,780  Epigravettian   0/17
Rochedane        France   13,090–12,830  Epipaleolithic  0/1
Ranchot 88       France   10,240–9,930   Mesolithic      0/2
Les Closeaux 13  France   10,240–9,560   Mesolithic      0/1
Berry-au-Bac     France   7,320–7,170    Mesolithic      0/1

OCA2, rs1800407, green or hazel eyes

Sample         Country  Years BP       Culture         D/T
Goyet Q116-1   Belgium  35,160–34,430  Aurignacian     0/7
Muierii 2      Romania  33,760–32,840  Unassigned      0/2
Paglicci 133   Italy    34,580–31,210  Gravettian      0/1
Věstonice 43   Czechia  30,710–29,310  Gravettian      0/1
Věstonice 16   Czechia  30,710–29,310  Gravettian      0/10
Ostuni 1       Italy    27,810–27,430  Gravettian      0/2
El Mirón       Spain    18,830–18,610  Magdalenian     0/5
Hohle Fels 79  Germany  15,070–14,270  Magdalenian     0/1
Villabruna     Italy    14,180–13,780  Epigravettian   1/21
Rochedane      France   13,090–12,830  Epipaleolithic  0/1
Ranchot 88     France   10,240–9,930   Mesolithic      0/1
Falkenstein    Germany  9,410–8,990    Mesolithic      0/1

OCA2, rs1800414, Mongoloid light skin

Sample           Country  Years BP       Culture         D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian     0/1
Muierii 2        Romania  33,760–32,840  Unassigned      0/1
Pavlov 1         Czechia  31,110–29,410  Gravettian      0/1
Věstonice 16     Czechia  30,710–29,310  Gravettian      0/2
El Mirón         Spain    18,830–18,610  Magdalenian     0/3
Afontova Gora 3  Russia   16,930–16,490  Unassigned      0/1
Hohle Fels 49    Germany  16,000–14,260  Magdalenian     0/1
Villabruna       Italy    14,180–13,780  Epigravettian   0/12
Rochedane        France   13,090–12,830  Epipaleolithic  0/2
Chaudardes 1     France   8,360–8,050    Mesolithic      0/1

OCA2/HERC2, rs12913832, blue eyes

Sample           Country  Years BP       Culture        D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian    0/1
Kostenki 12      Russia   32,990–31,840  Unassigned     0/1
Věstonice 16     Czechia  30,710–29,310  Gravettian     0/5
Ostuni 1         Italy    27,810–27,430  Gravettian     0/2
El Mirón         Spain    18,830–18,610  Magdalenian    0/5
Afontova Gora 3  Russia   16,930–16,490  Unassigned     0/1
Goyet Q-2        Belgium  15,230–14,780  Magdalenian    0/1
Villabruna       Italy    14,180–13,780  Epigravettian  11/11
Ranchot 88       France   10,240–9,930   Mesolithic     1/1
Falkenstein      Germany  9,410–8,990    Mesolithic     1/1

SLC24A5, rs1426654, Caucasoid light skin

Sample      Country  Years BP       Culture        D/T
Ostuni 1    Italy    27,810–27,430  Gravettian     0/1
El Mirón    Spain    18,830–18,610  Magdalenian    0/1
Villabruna  Italy    14,180–13,780  Epigravettian  0/5
Ranchot 88  France   10,240–9,930   Mesolithic     0/1

SLC45A2, rs16891982, Caucasoid light skin

Sample           Country  Years BP       Culture        D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian    0/6
Muierii 2        Romania  33,760–32,840  Unassigned     0/1
Věstonice 13     Czechia  31,070–30,670  Gravettian     0/1
Věstonice 16     Czechia  30,710–29,310  Gravettian     1/18
El Mirón         Spain    18,830–18,610  Magdalenian    0/11
Afontova Gora 3  Russia   16,930–16,490  Unassigned     0/2
Villabruna       Italy    14,180–13,780  Epigravettian  0/54
Ranchot 88       France   10,240–9,930   Mesolithic     0/3

TYR, rs1042602, light skin, absence of freckles

Sample           Country  Years BP       Culture        D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian    0/5
Věstonice 43     Czechia  30,710–29,310  Gravettian     0/2
Věstonice 16     Czechia  30,710–29,310  Gravettian     0/16
Ostuni 1         Italy    27,810–27,430  Gravettian     0/4
El Mirón         Spain    18,830–18,610  Magdalenian    0/8
Afontova Gora 3  Russia   16,930–16,490  Unassigned     0/1
Brillenhöhle     Germany  15,120–14,440  Magdalenian    0/2
Villabruna       Italy    14,180–13,780  Epigravettian  0/29
Ranchot 88       France   10,240–9,930   Mesolithic     0/3

TYR, rs1393350, blond hair, blue eyes

Sample         Country  Years BP       Culture         D/T
Goyet Q116-1   Belgium  35,160–34,430  Aurignacian     0/2
Muierii 2      Romania  33,760–32,840  Unassigned      0/1
Věstonice 43   Czechia  30,710–29,310  Gravettian      0/1
Věstonice 16   Czechia  30,710–29,310  Gravettian      0/12
Ostuni 1       Italy    27,810–27,430  Gravettian      0/2
El Mirón       Spain    18,830–18,610  Magdalenian     0/9
Hohle Fels 49  Germany  16,000–14,260  Magdalenian     0/1
Villabruna     Italy    14,180–13,780  Epigravettian   0/35
Rochedane      France   13,090–12,830  Epipaleolithic  0/2
Ranchot 88     France   10,240–9,930   Mesolithic      0/2
Falkenstein    Germany  9,410–8,990    Mesolithic      0/1
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52 comments on “Phenotype SNPs from Ice Age Europe
  1. norah4you says:

    Reblogged this on Norah4you's Weblog and commented:
    A special thanks to Genetiker who allows me to reblogg this. Please note Ranchot 88. Ranchot is located so the area with ancient prehistoric caves naturally is connecting Rhône valley with Rhen valley. If you take a closer look at the artifacts from Mesolithic period round 10,000 you will find interesting things to “dig” deeper in using Genetiker’s results for such a study.

  2. Anom says:

    Disappointing to say the least, I was expecting more light features in the paleolithic like modern northern/central Europeans, Motala HGs and Samara HG had, thinking they would’ve been the people who stayed behind in ice age refuges while the typical WHGs like La Brana retreated to warmer climates, lost their light pigmentation, came back up when the ice retreated and didn’t wind up contributing much to the modern European genepool.

    I guess the mainstream theory of light hair/etc evolving in cold conditions given Goyet’s red hair but being selected for to make up a majority recently holds true, but I still don’t know why this would happen. It wasn’t farming, given light skin is found in Siberian Afontova Gora 17k years ago and light hair in Motala HGs and Samara HG which obviously weren’t involved in farming. There’s still no clear source of light pigmentation. I still have doubts about determining pigmentation from even the highest coverage ancient samples(and some of these are pretty low) given a modern human will have much more SNPs.

    Having the “latest” and newest human features isn’t a bad thing at all, quite the opposite, it’s just nice to have some longevity or know the source of it.

    • Genetiker says:

      given Goyet’s red hair

      The derived allele of rs11547464 for Goyet Q56-16 is from a single read, five bases away from the end base of the read. So it’s probably just DNA damage.

      but I still don’t know why this would happen

      Sexual selection.

      Darwin believed that many of the differences between the races are due to sexual selection. From The Descent of Man:

      We know, however, from the many facts already given that the colour of the skin is regarded by the men of all races as a highly important element in their beauty; so that it is a character which would be likely to have been modified through selection, as has occurred in innumerable instances with the lower animals.

      We have seen that with the lowest savages the people of each tribe admire their own characteristic qualities,—the shape of the head and face, the squareness of the cheek-bones, the prominence or depression of the nose, the colour of the skin, the length of the hair on the head, the absence of hair on the face and body, or the presence of a great beard, and so forth. Hence these and other such points could hardly fail to be slowly and gradually exaggerated, from the more powerful and able men in each tribe, who would succeed in rearing the largest number of offspring, having selected during many generations for their wives the most strongly characterised and therefore most attractive women. For my own part I conclude that of all the causes which have led to the differences in external appearance between the races of man, and to a certain extent between man and the lower animals, sexual selection has been the most efficient.

      There’s still no clear source of light pigmentation.

      Random mutation—the raw material of evolution, acted upon by sexual selection.

      • Anom says:

        I still like to think it’s simply adaptation to the environment and lack of UV ray/sunlight exposure, rather than just some random mutation, as most mutations seem to have a reason behind them, although your theory and the mainstream one are more likely(I’ll freely admit I know little to nothing about genetics and evolution anyway).

        Vestonice16 and Villabruna are both on GEDMatch right now, Villabruna was a typical WHG with little exotic components(well, none on Eurogenes K15, and he even had more North Sea than other WHGs at 40, Hiriplex also says he had light brown hair based on your phenotype SNPs, while most WHGs had black hair), while Vestonice16 was the typical archaic human with high amounts of South Asian and a plethora of other human ancestries, and was dark pigmented. This is most likely why the original nature paper puts them into clusters, they aren’t not descendant from eachother, the later ones are simply different because of genetic drift.

        It could simply be these early, southern human genetic components were blocking the evolution or selection of light features, and selection for light hair/etc only started when we genetically drifted away from the archaic human components like South Asian. That could be why paleolithic Europeans had brown eyes. As for why modern Native Americans and East Asians are dark pigmented even though they’re up in cold climates with little sun exposure, it could be their higher Neanderthal blocking it(paleolithic Europeans also had higher Neanderthal admixture) or it’s a Scandinavian/Central Europe climate which produces light eyes/light hair, not an arctic climate, which East Asians are undoubtably derived from given their slanted eyes to protect from snow blindness.

        That’s just my take on it, I probably have no idea what I’m talking about, I just hate the idea of it being some “random” mutation without a purpose. Thanks for your work again, btw. I eagerly await your admixture results for these samples.

  3. Olympus Mons says:

    I am even afraid to ask…. how to read the AA, GG TT and so forth. 😉

  4. “Note that some of the derived alleles may be based on single reads, and they may be near the ends of reads, which are often affected by DNA damage.”

    How many reads at rs1805007 and rs1805008 did you get for the Motala HGs?

    • Genetiker says:

      For rs1805007, I0012 had the derived allele for 1 out of 7 reads, and it was at the very end of the read. I0016 had the derived allele for 1 out of 10 reads.

      For rs1805008, I0016 had the derived allele for 1 out of 8 reads.

      So the odds are not good that they really had those derived alleles.

  5. Geneticker thanks for gathering phenotype SNPs and Y SNPs, no one else posts them like you do. I’ve collected all your work in spreadsheets. Maybe you should list the amount of reads you get for individuals for each SNP and how many times they get a derived allele.

    Concerning Red hair MC1R SNPs, I know of many other 16th chromsome SNPs that are in a haplotype with those MC1R SNPs. You can test those to confirm if a derived allele call in a MC1R SNPs is legitimate or not.

    The only confirmed(with enough coverage) derived alleles in Red hair MC1R SNPs are from Late Neolithic/Bronze age Sweden, Germany, and Kazakhstan(Sintashta). But you list many individuals from Neolithic Anatolia and Yamnaya. I’ll give you their IDs so you can check how many reads they get derived alleles in.

    It looks like Red hair was very rare in all of European’s Stone age ancestors. If so that’s an interesting development. It would probably mean the very high frequency in Northern Europe(esp. British Isles and Scandinavia) today is the result of natural selection favoring Red hair in Bronze age Europe.

    Yeah, I know what you’re thinking Red hair is rare. However, about 40% of British and Scandinavian carry the gene and about 20% of their men have Red facial hair. So, before modern times you’d see a lot of Red beards and are today because beards are back in style. It looks like it is a lot more frequent than it was in any of their Stone age ancestors.

    • Genetiker says:

      Maybe you should list the amount of reads you get for individuals for each SNP and how many times they get a derived allele.

      I’ve thought about it.

      It would probably mean the very high frequency in Northern Europe(esp. British Isles and Scandinavia) today is the result of natural selection favoring Red hair in Bronze age Europe.

      It’s the result of sexual selection. And I think that there were populations in Europe with blond and red hair before the Bronze Age.

      Here are the derived allele counts and read positions for some more samples:

      rs1805007:

      Asia Minor Neolithic I1581: 1/5, middle

      Bell Beaker Germany I0113: 1/3, middle

      Halberstadt LBA I0099: 9/18

      Khvalynsk I0122: 1/2, 4 from end base

      Pit Grave Samara I0438: 1/2, very end

      Unetice EBA I0117: 1/4, middle

      rs1805008:

      Asia Minor Neolithic I0708: 1/9, middle

      Asia Minor Neolithic I0744: 1/4, very end

      Asia Minor Neolithic I1099: 1/6, 5 from end base

      Asia Minor Neolithic I1585: 1/5, 7 from end base

      Iberia Copper Age I1300: 1/8, very end

      Timber Grave I0232: 2/15, 1 from end base, middle

      So it’s likely that none of the samples really had the rs1805008 derived allele. And it’s unlikely that the Asia Minor Neolithic, Khvalynsk, and Pit Grave samples had the rs1805007 derived allele. The Halberstadt sample definitely had it. The Bell Beaker sample probably had it, and the Unetice sample might have also had it.

      • Wow, awesome thanks a lot Geneticker. Sexual selection for Red hair? Sounds a little crazy. However, I guess if more ancient DNA confirms the trend we are seeing there may be no other explanation. That’ll shut up any Ginger haters. It looks like if anything Gingers prospered and were considered attractive in Bronze age Europe 🙂

  6. vsva says:

    Genetiker,can you show us y snp calls from other samples from ice age europe and from neolithic barcin(matthieson study)? please.

    • Genetiker says:

      I analyzed all of the Ice Age Y-DNA samples, but aside from the samples listed in my last post, I didn’t learn anything significant beyond what appeared in the paper.

      I gave the calls for the I0724 Asia Minor Neolithic sample in this post. It didn’t look like anything interesting could be learned from the other Asia Minor Neolithic samples.

      If you have questions about specific samples, I can answer them.

  7. Denis Anderthal says:

    Does anyone have any explanation for why we have so many phenotype SNPs from these new samples, yet none from the very well-preserved skeleton of Kennewick Man, and just the minimum amount of markers to test for his ancestry?

    • Genetiker says:

      Here are the phenotype SNPs for Kennewick Man:

      Gene        SNP         Genotype  Phenotype
      ASIP        rs6058017   AA        Veddoid brown skin
      EDAR        rs3827760   GG        Mongoloid teeth, hair, etc.
      IRF4        rs12203592  CC        light hair and eyes, freckling
      KITLG       rs642742    CC        Veddoid brown skin
      MC1R        rs11547464  GG        red hair
      MC1R        rs1805005   GG        blond hair, fair skin
      MC1R        rs1805007   CC        red hair, fair skin
      MCM6        rs4988235   AA        ability to digest milk
      OCA2/HERC2  rs12913832  AA        blue eyes
      OCA2        rs1800407   CC        green or hazel eyes
      OCA2        rs1800414   TT        Mongoloid light skin
      SLC24A5     rs1426654   GG        Caucasoid light skin
      TYRP1       rs2733831   AA        light hair and eyes
      TYR         rs1393350   GG        blond hair, blue eyes
      

      And yes, the lactase persistence allele is DNA damage. Based on one read, and seven bases from the end base.

      And there’s plenty of data for Kennewick Man. 3.2 gigabytes of it.

      There never was any solid evidence that Kennewick Man was Caucasoid, and there’s no conspiracy to cover up the truth about him.

      It’s baffling to me that so many people seized upon Kennewick Man as evidence of Caucasoids in the Americas before the Vikings, based on no real evidence, while at the same time there are piles of incontrovertibly European remains all over Peru, many of which are just lying around on the ground for everybody to see, which nobody seems to want to talk about.

      Peru is where the evidence for Europeans in the Americas before the Vikings is located, and that’s where the conspiracy to cover up the truth is taking place. I’ve said before that the academic establishment will do anything and everything to cover up the truth about Whites in ancient Peru, including fabricating and falsifying data, and indeed it looks like David Reich and his associates have just such a colossal fraud in preparation.

      • Denis Anderthal says:

        Thanks very much for the post. I didn’t know there was that much data available on him. I’m still not completely convinced though that Kennewick Man didn’t have some ancient European admixture. He shifts more to Europe than Anzick 1 does on most analysis of covariance and classification plots and graphs I’ve seen. His mtdna X2a seems more likely to me to have come from across the Atlantic than by Siberia. So far, X2 has been found in ancient dna samples in Europe and not in Eastern Eurasia, at least not yet. Also, with Villabruna we now have an R1b1a in Italy 14,000 years ago. And this might add weight to a trans-atlantic crossing of R1b-M269 accompanying that X2. On page 768 of this paper: http://www.academia.edu/9562579/Solutrean_hypothesis_genetics_the_mammoth_in_the_room it mentions Native American R1 STR derived values being different from those found in Europe. And also, X2a was found in Windover, Florida at roughly the same time as when Kennewick Man lived, so as not discrediting the theory that X2a may have spread from the East in America as its current distribution lends weight to, as is also the case with R1.

      • Capra Internetensis says:

        Thanks for those Kennewick man SNPs! Very nice to see these done for Paleo-Indians.

        Is that a typo or is he really GG in EDAR rs3827760? The ancestral allele is T and the usual derived allele is C.

        Do you know if there’s a read for Anzick-1’s rs3827760? I’ve never seen one.

  8. Genetiker says:

    I’ve updated this post to give derived allele counts and total numbers of reads instead of genotype calls.

    I’ll soon update my previous phenotype SNP posts to also give derived allele counts.

  9. Genetiker says:

    What about calls of two T1a samples from Karsdorf? Did you identfied subclade?

    I0795 was positive for one T1a1-L162 SNP, CTS880, and negative for another, CTS11698.

    I0797 didn’t have any positive calls downstream of T1-L206. He was negative for a T1a1-L162 SNP, Y3789/FGC3966.

    Also i am intersted in ciclovina, Kostenki12 and krems y snp calls.

    For Cioclovina 1 I have one positive CT SNP, and then just a few obviously wrong SNPs downstream of that.

    Kostenki 12 is positive for 4 C SNPs and negative for 3. He’s positive for a C1 SNP. He’s positive for 2 F SNPs and negative for 2. He’s negative for a bunch of IJ and I SNPs. He’s negative for two K(xLT)-M2335 SNPs. He’s positive for K2b-M1205. He’s positive for 1 P SNP and negative for 4. Considering that Kostenki 14 was C1b1-K281*, I think Kostenki 12 was most likely also C1.

    I hadn’t noticed that Krems WA3 was a male sample for which no Y haplogroup was given in the table in the paper. He belonged to I, and I’ve added a link to his calls in my previous post.

  10. Genetiker says:

    I’ve updated my post More phenotype SNPs from prehistoric Eurasia to give derived allele counts.

  11. Genetiker says:

    What about Barcin G2a samples? Is one of them L497+ or L1266?

    No.

    What haplogroup is goyet-q2(Magdalenian sample)?

    Some calls for Goyet Q-2:

    HIJK-PF3494/F929/M578
    H-Z4278/M2945
    H-P96-Z19014
    H-P96-Z19016
    IJ-Y1905/FGC1571
    IJ-Y1844/PF3511/FGC1586
    I-PF3640
    I-PF3817
    I-PF3837
    I1-Z2823
    I1-Z2887
    I2-L460-P37-CTS595-S21825-S21204
    I2-L460-P37-CTS595-S21825-Z24429/Y4265
    I2-L460-P37-CTS595-L158-PF3825

    So he had a couple of positive H calls, but since the other two Magdalenian samples were I, he was more likely to have also been I.

  12. vsva says:

    There were three P303 samples from Barcin, which one of them is CTS342 by authors.there are only P303(cts342) or deeper subclade?

  13. Genetiker says:

    And what other P303 samples?

    I0744 is positive for G2a2b2a6-Z6030. I1097 is positive for G2a2b2a3-Z39318.

    Its supposed to be i1284.

    I1284 isn’t I2c. It’s I2a(xI2a1b, I2a2a).

    • vsva says:

      G2a-z6030 and z39318 are some minority P303 branches? I saw some Sardinians. what about les chaudardes, Berry au Bac, Burkhardtshohle, Hohefels49 and rest El Mirador samples y snp calls? Thank you.

      • Genetiker says:

        G2a-z6030 and z39318 are some minority P303 branches?

        Yes.

        what about les chaudardes, Berry au Bac, Burkhardtshohle, Hohefels49 and rest El Mirador samples y snp calls?

        Hohle Fels 49 doesn’t have any positive calls downstream of I.

        Burkhardtshöhle is negative for four I1 SNPs and one I2 SNP.

        Chaudardes 1 is positive for an I2 SNP.

        Berry-au-Bac is positive for an I2a1b SNP.

        I1282 is I2(xI2a1a1, I2a1a2, I2a1b, I2a2). The other El Mirador samples already have sufficiently detailed haplogroups.

  14. Genetiker says:

    Is that a typo or is he really GG in EDAR rs3827760? The ancestral allele is T and the usual derived allele is C.

    T and C are the alleles on the reverse strand. A and G are the alleles on the forward strand.

    Do you know if there’s a read for Anzick-1’s rs3827760? I’ve never seen one.

    Here are the phenotype SNPs for Anzick 1:

    Gene        SNP         Genotype  Phenotype
    ASIP        rs2424984   TT        Veddoid brown skin
    ASIP        rs6058017   AA        Veddoid brown skin
    ASIP        rs6119471   CC
    EDAR        rs3827760   GA        Mongoloid teeth, hair, etc.
    EXOC2       rs4959270   CA
    IRF4        rs12203592  CC        light hair and eyes, freckling
    KITLG       rs12821256  TT        blond hair
    KITLG       rs642742    CC        Veddoid brown skin
    MC1R        rs1110400   TT        red hair
    MC1R        rs11547464  GG        red hair
    MC1R        rs1805005   GG        blond hair, fair skin
    MC1R        rs1805006   CC        red hair, fair skin
    MC1R        rs1805007   CC        red hair, fair skin
    MC1R        rs1805008   CC        red hair, fair skin
    MC1R        rs1805009   GG        red hair, fair skin
    MC1R        rs2228479   GG
    MC1R        rs885479    GG
    MCM6        rs182549    CC        ability to digest milk
    MCM6        rs4988235   GG        ability to digest milk
    OCA2/HERC2  rs12913832  AA        blue eyes
    OCA2        rs1545397   TT
    OCA2        rs1800407   CC        green or hazel eyes
    OCA2        rs1800414   TT        Mongoloid light skin
    PIGU/ASIP   rs2378249   AA
    SLC24A4     rs12896399  GG
    SLC24A4     rs2402130   AA
    SLC24A5     rs1426654   GG        Caucasoid light skin
    SLC45A2     rs16891982  CC        Caucasoid light skin
    SLC45A2     rs28777     CC
    TYRP1       rs2733831   GA        light hair and eyes
    TYRP1       rs683       CA
    TYR         rs1042602   CC        light skin, absence of freckles
    TYR         rs1393350   GG        blond hair, blue eyes
    

    The derived allele count for rs3827760 is 18/38. The derived allele count for rs2733831 is 3/7.

  15. Capra Internetensis says:

    Thanks!

  16. vsva says:

    Yes, most samples are I2a1, I2a2 or G2a2b, but there is at least one sample with only G2a. What subclade it is?

  17. vsva says:

    I found another three male samples from Ice age Europe wihout given y dna haplogroup by authors(Iboussieres39, Brillenhohle and Hohefels79). What about them?

  18. Genetiker says:

    And what about Vestonice 15? I saw some information that is A1b.

    Yes, it’s A1b. And as the paper reported, it’s BT. It’s also CT. And it has negative calls for one C SNP, two V86-equivalent SNPs, four F SNPs, and one I SNP.

  19. vsva says:

    Can i ask about some other samples y snp calls? What about one Esperstedt sample i0807(not i0172 I2a1B1 l161), one Els Trocs i0411 listed only as F, i0551 Salzmunde and Barcin samples i1099, i1103, i1583, i0723 and i0727.

    • Genetiker says:

      I0807: I2, possibly I2a2a2-S23467
      I0411: R1b1a, probably V88, not V35
      I0551: G2a2a1-Z6199
      I1099: G2a2a1a2a2-FGC2315
      I1103: G2a2a1a2a-PF3237
      I1583: G2a2a1a2a2-FGC2315
      I0723: G2a2a1-Z6042
      I0727: G, negative for 3 G1 and 3 G2 SNPs

  20. vsva says:

    What subclade are samples El Mirador i1274, i1277,Halberstadt i0048 and 0056 and Srubnaya samples i0423, i0424 and one Scythian sample?

    • Genetiker says:

      I1274: I2a2a2a-S24785
      I1277: I2a2a2a-L1228
      I0048: G2a2a1-Z6042
      I0056: G2a2a-PF3147
      I0423: R1a1a1b2a-Z95
      I0424: R1a1a1b2a2-Z2121
      I0247: R1a1a1b2a2a-Z2123

  21. vsva says:

    What y SNP calls are samples i0406 La Mina, i1303 El Mirador, i0432 Poltavka outlier, i0099 Halberstadt, i0419 Potapovka?

  22. […] Phenotype SNPs from Ice Age Europe […]

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