A very interesting new paper by Wilde et al. 2014 tested three genes (HERC2, SLC45A2 and TYR) associated with skin, eye and hair pigmentation in 63 ancient samples from the Pontic-Caspian Steppe (mostly modern Ukraine) dating from the Chalcolithic and Bronze Age.
The results are relatively surprising. Mutations in SLC24A5, another gene for fair skin related to SLC45A2, has previously been associated with the spread of Neolithic farmers and Bronze Age Steppe people (Proto-Indo-Europeans). This paper tested SLC45A2, a gene that mediates melanin synthesis. The authors found it to be present in only 43% of the samples. Nearly 100% of modern Europeans possess the light skin variant for both the SLC24A5 and SLC45A2 genes.
One gene alone isn't enough to determine skin colour with certainty. But it probably means that the Proto-Indo-Europeans possessed various shades of skin colour. That may be the result of the very composite nature of the Bronze Age Steppe people, who I believe belonged to a mixture of Y-haplogroups indigenous East European R1a, East Anatolian R1b, and other Near Eastern haplogroups (G2a3b1, J2b2, T1a1a) that may have come through the Balkans/Carpathians.
That SLC24A5 mutation was absent from Mesolithic samples from Spain and Luxembourg, although they did possess the HERC2 mutation. What we can say is that fair skin was positively selected in Europeans in the last 5000 years. We still don't know when this mutation reached fixation (nearly 100%) in the European population. It has struck me before that ancient Romans and Etruscans appeared to have had much darker skin than modern southern Europeans. That could mean that fair skin only became a common feature throughout Europe during the Middle Ages, perhaps in part due to the influx of Germanic and Slavic people into the Roman Empire. Fair pigmentation would presumably have been positively selected more quickly in Northern Europe for reasons of adaptation.
The frequency of the two other genes, HERC2 and TYR, came as an even bigger surprise, as a mere 16% and 4% of Bronze Age Steppe people possessed them. Their modern frequency in Europe is, in all fairness (pun intended), also lower than SLC45A2, being found respectively in 71% and 36% of Europeans. Unfortunately I do not have data on their regional distribution in Europe, nor in the Middle East.
The article mentions that the TYR mutation (rs1042602) is highly polymorphic in Europeans. According to the HapMap data, Tuscans (TSI) have a higher frequency of the derived allele than Northwest Europeans (CEU).
The HERC2 mutation (rs12913832) is associated with skin pigmentation, but especially with eye colour (the GG allele corresponding to blue eyes 99% of the time). So blue eyes were present among Proto-Indo-Europeans, but at low frequency. Blue eyes might have been more common among Mesolithic Europeans, at least in the Atlantic and Baltic region. The 16% of HERC2 in the Pontic Steppe would have come from the genes maternally inherited from Mesolithic Europeans (U2, U4, U5).
On a side note, it is highly frustrating that this team of geneticists tested 63 samples from the Yamna and Catacomb and related cultures and did not test any Y-DNA at all ! This could prove once and for all that R1b people spread from the Pontic Steppe and not with Neolithic Near Eastern farmers as so many academic papers have claimed.
Nevertheless, the supplementary information provides a list of all the samples tested with their location and age, and mtDNA haplogroups, which is quite useful. But the study would have been much more interesting if they had also provided the Y-DNA haplogroups for each sample. We would have been able to determine whether there was an ethnic heterogeneity in the Steppe population 5000 years ago. I have always suspected that R1a tribes lived in the northern forest-steppe during the Yaman period, while R1b lived in coastal areas and in the Northwest Caucasus. G2a3b would also be in the Northwest Caucasus, but I am not so sure about J2b2 and T1a1a.
UPDATE:
Of the 47 samples tested for the HERC2 mutation, only four had the GG allele for blue eyes. Two of them were from the Yamna culture (one from Kalinovka I near Samara in the Lower Volga region, and one from Mayaki near Odessa in southwest Ukraine) and two from the subsequent Catacomb culture (both from Novozvanovka II, near Donetsk in eastern Ukraine). Five other samples were AG, three from the Yamna culture and two from the Catacomb culture. All the Chalcolithic samples were AA (brown eyes). The sample size is small, but that could mean that blue eyes were not present in the Pontic Steppe before the Early Bronze Age, and that there was therefore a migration of people from outside the steppes, or a dramatic expansion from one small part of the steppes.
Only three samples had the TYR mutation. There were two from the Yamna culture, including one that was homozygous (AA). The other one was from the Catacomb culture. Once again, none of the Chalcolithic samples were derived.
Interestingly, the AA sample (KAL1) was also from the Kalinovka I site, but that one was AG for the HERC2 gene, not GG like KAL2. Surprisingly that KAL1 individual belong to mtDNA N1a1a (the only one in all the samples), which is more typical of Southwest Asian Neolithic farmers than of PIE speakers. But the SLC45A2 allele (CC) suggests that he/she had dark skin.
Only 22 samples were tested for the SLC45A2 mutation (rs16891982). The European allele for white skin is GG, which was found in 5 Yamna individuals and one Catacomb skeleton. There were seven other samples that were CG, 3 Yamna, 3 Catacomb, and interestingly one Early Chalcolithic too. The Chalcolithic sample was from Vinogradnoe in southern central Ukraine. It was in the same kurgan as a Yamna and a Catacomb sample that were also CG. That could be a sign of unusual continuity in population in that particular area. But it could also mean that the dating is wrong and that it is Yamna too.
Here is the breakdown of mtDNA haplogroups by period. I don't understand why the authors just listed haplogroup U without mentioning at least the top subclade. They had the data. I have added it myself.
Early Chalcolithic
SMY3 : H (rCRS)
SMY4 : H5
SMY9 : H7a1 or H13
SMY11 : T2e
VIN1 : H (rCRS)
Late Chalcolithic
DUR1 : U5a2a
MAJ8 : T2
MAJ9 : W
MOB1 : U5a1
MOB3 : U5a1
Yamna
BEN3 : H33c
KAL1 : N1a1a
KAL2 : H*
MAJ3 : U5a1
MAJ4 : U5b2
MAJ5 : X2h (?)
NIK1 : T1a
NIK7 : H (rCRS)
OLE1 : T2
OLE7 : J2b
OVI2 : K
OVI3 : U/K
PEJ1 : U5a1
PES7 : H1a1 or H5a1j
POD1 : W6
POD2 : T2
POP1 : T2a1b
POP3 : U2e
POP4 : U5a1
RIL3 : K1
SUG2 : I1a
SUG6 : H1, H3 or H6
SUG7 : H (rCRS)
SUG8 : H (rCRS)
TET2 : U4a1
VIN2 : T1a
VIN5 : T1a
VIN12 : T1
Catacomb
KNO4 : U4
LIS1 : U5a1
LIS2 : U4
LIS3 : H2a1
NEV1 : U5a1
NEV3 : H1, H3 or H6
NOZ1 : U4
NOZ2 : U4
PEJ2 : H1 or H13
PEJ3 : H1, H3 or H6
PEJ4 : H1, H3 or H6
PEJ5 : U4
SAC2 : J2b
SUG5 : H6
TEM1 : U4
TEM2 : H (rCRS)
TEM3 : J1b1a1
TEM4 : U5a1
TEM5 : R1a
TEM6 : R1a
TEM7 : U4
TEM8 : U (?)
TET1 : I1d
VIN3 : U5a1
VIN8 : J1b1a1
Points of interest:
- U5a is found in all periods. All the Bronze Age samples are U5a1, which I have described as the main Indo-European subclade of U5 (although of Mesolithic Northeast European origin).
- Haplogroup T is oddly absent from the Catacomb samples. T1a, which I have linked to the spread of PIE people, is found in several Yamna samples. Chalcolithic samples only have T2, including T2e (also found in LBK samples from Neolithic Germany).
- J1b1a1, one of the maternal lineages most strongly associated with the original pre-IE R1b people in the Near East, is found in two Catacomb samples.
- Haplogroups I and W, which are both strongly associated with PIE migrations, are indeed found in Bronze Age samples, and W even in a Late Chalcolithic sample.
- Note the absence of haplogroup V, which has been very elusive in ancient samples from all periods.
- The Early Chalcolithic samples look very much like Near Eastern farmers. I would expect that these lineages (H5, H7, T2e) represent the arrival of G2a3, J2b2 and T into the Pontic Steppe from the Carpathians or Balkans.
- The Late Chalcolithic samples look much more native Europeans, and probably represent the descendants of the Mesolithic inhabitants of the steppes (I2a1 and/or R1a), or new immigrants from the north.
- Apart from one U4a1 sample from Yamna in Moldova, U4 is found exclusively in Catacomb samples and at extremely high frequency (28%). This tends to confirm my hypothesis that Yamna was an R1b-dominant culture or mixed R1a-R1b, and that R1a tribes from the north invaded the Pontic Steppe from central European Russia and the Volga-Ural during the Catacomb culture. U4 strongly correlates with R1a and peaks in the Volga-Ural region today.
- Overall, the Yamna samples look quite similar to those from the Corded Ware culture. Therefore there might have been more R1a in the Yamna culture that I expected. In that case, the bulk of R1b would have been in the Maykop culture or in very coastal parts of the Pontic Steppe. I believe that the J1b1a samples (TEM3 and VIN8) are the most reliable proxy for Y-DNA R1b. The samples are from Vinogradnoe, immediately north of Crimea, and Temrta in southern Russia, between the North Caucasus and Kalmykia (only about 250 km from Maykop). TEM3 was not tested for autosomal DNA, but VIN8 had apparently dark skin. However it is one of the three samples derived for the TYR gene.
The results are relatively surprising. Mutations in SLC24A5, another gene for fair skin related to SLC45A2, has previously been associated with the spread of Neolithic farmers and Bronze Age Steppe people (Proto-Indo-Europeans). This paper tested SLC45A2, a gene that mediates melanin synthesis. The authors found it to be present in only 43% of the samples. Nearly 100% of modern Europeans possess the light skin variant for both the SLC24A5 and SLC45A2 genes.
One gene alone isn't enough to determine skin colour with certainty. But it probably means that the Proto-Indo-Europeans possessed various shades of skin colour. That may be the result of the very composite nature of the Bronze Age Steppe people, who I believe belonged to a mixture of Y-haplogroups indigenous East European R1a, East Anatolian R1b, and other Near Eastern haplogroups (G2a3b1, J2b2, T1a1a) that may have come through the Balkans/Carpathians.
That SLC24A5 mutation was absent from Mesolithic samples from Spain and Luxembourg, although they did possess the HERC2 mutation. What we can say is that fair skin was positively selected in Europeans in the last 5000 years. We still don't know when this mutation reached fixation (nearly 100%) in the European population. It has struck me before that ancient Romans and Etruscans appeared to have had much darker skin than modern southern Europeans. That could mean that fair skin only became a common feature throughout Europe during the Middle Ages, perhaps in part due to the influx of Germanic and Slavic people into the Roman Empire. Fair pigmentation would presumably have been positively selected more quickly in Northern Europe for reasons of adaptation.
The frequency of the two other genes, HERC2 and TYR, came as an even bigger surprise, as a mere 16% and 4% of Bronze Age Steppe people possessed them. Their modern frequency in Europe is, in all fairness (pun intended), also lower than SLC45A2, being found respectively in 71% and 36% of Europeans. Unfortunately I do not have data on their regional distribution in Europe, nor in the Middle East.
The article mentions that the TYR mutation (rs1042602) is highly polymorphic in Europeans. According to the HapMap data, Tuscans (TSI) have a higher frequency of the derived allele than Northwest Europeans (CEU).
The HERC2 mutation (rs12913832) is associated with skin pigmentation, but especially with eye colour (the GG allele corresponding to blue eyes 99% of the time). So blue eyes were present among Proto-Indo-Europeans, but at low frequency. Blue eyes might have been more common among Mesolithic Europeans, at least in the Atlantic and Baltic region. The 16% of HERC2 in the Pontic Steppe would have come from the genes maternally inherited from Mesolithic Europeans (U2, U4, U5).
On a side note, it is highly frustrating that this team of geneticists tested 63 samples from the Yamna and Catacomb and related cultures and did not test any Y-DNA at all ! This could prove once and for all that R1b people spread from the Pontic Steppe and not with Neolithic Near Eastern farmers as so many academic papers have claimed.
Nevertheless, the supplementary information provides a list of all the samples tested with their location and age, and mtDNA haplogroups, which is quite useful. But the study would have been much more interesting if they had also provided the Y-DNA haplogroups for each sample. We would have been able to determine whether there was an ethnic heterogeneity in the Steppe population 5000 years ago. I have always suspected that R1a tribes lived in the northern forest-steppe during the Yaman period, while R1b lived in coastal areas and in the Northwest Caucasus. G2a3b would also be in the Northwest Caucasus, but I am not so sure about J2b2 and T1a1a.
UPDATE:
Of the 47 samples tested for the HERC2 mutation, only four had the GG allele for blue eyes. Two of them were from the Yamna culture (one from Kalinovka I near Samara in the Lower Volga region, and one from Mayaki near Odessa in southwest Ukraine) and two from the subsequent Catacomb culture (both from Novozvanovka II, near Donetsk in eastern Ukraine). Five other samples were AG, three from the Yamna culture and two from the Catacomb culture. All the Chalcolithic samples were AA (brown eyes). The sample size is small, but that could mean that blue eyes were not present in the Pontic Steppe before the Early Bronze Age, and that there was therefore a migration of people from outside the steppes, or a dramatic expansion from one small part of the steppes.
Only three samples had the TYR mutation. There were two from the Yamna culture, including one that was homozygous (AA). The other one was from the Catacomb culture. Once again, none of the Chalcolithic samples were derived.
Interestingly, the AA sample (KAL1) was also from the Kalinovka I site, but that one was AG for the HERC2 gene, not GG like KAL2. Surprisingly that KAL1 individual belong to mtDNA N1a1a (the only one in all the samples), which is more typical of Southwest Asian Neolithic farmers than of PIE speakers. But the SLC45A2 allele (CC) suggests that he/she had dark skin.
Only 22 samples were tested for the SLC45A2 mutation (rs16891982). The European allele for white skin is GG, which was found in 5 Yamna individuals and one Catacomb skeleton. There were seven other samples that were CG, 3 Yamna, 3 Catacomb, and interestingly one Early Chalcolithic too. The Chalcolithic sample was from Vinogradnoe in southern central Ukraine. It was in the same kurgan as a Yamna and a Catacomb sample that were also CG. That could be a sign of unusual continuity in population in that particular area. But it could also mean that the dating is wrong and that it is Yamna too.
Here is the breakdown of mtDNA haplogroups by period. I don't understand why the authors just listed haplogroup U without mentioning at least the top subclade. They had the data. I have added it myself.
Early Chalcolithic
SMY3 : H (rCRS)
SMY4 : H5
SMY9 : H7a1 or H13
SMY11 : T2e
VIN1 : H (rCRS)
Late Chalcolithic
DUR1 : U5a2a
MAJ8 : T2
MAJ9 : W
MOB1 : U5a1
MOB3 : U5a1
Yamna
BEN3 : H33c
KAL1 : N1a1a
KAL2 : H*
MAJ3 : U5a1
MAJ4 : U5b2
MAJ5 : X2h (?)
NIK1 : T1a
NIK7 : H (rCRS)
OLE1 : T2
OLE7 : J2b
OVI2 : K
OVI3 : U/K
PEJ1 : U5a1
PES7 : H1a1 or H5a1j
POD1 : W6
POD2 : T2
POP1 : T2a1b
POP3 : U2e
POP4 : U5a1
RIL3 : K1
SUG2 : I1a
SUG6 : H1, H3 or H6
SUG7 : H (rCRS)
SUG8 : H (rCRS)
TET2 : U4a1
VIN2 : T1a
VIN5 : T1a
VIN12 : T1
Catacomb
KNO4 : U4
LIS1 : U5a1
LIS2 : U4
LIS3 : H2a1
NEV1 : U5a1
NEV3 : H1, H3 or H6
NOZ1 : U4
NOZ2 : U4
PEJ2 : H1 or H13
PEJ3 : H1, H3 or H6
PEJ4 : H1, H3 or H6
PEJ5 : U4
SAC2 : J2b
SUG5 : H6
TEM1 : U4
TEM2 : H (rCRS)
TEM3 : J1b1a1
TEM4 : U5a1
TEM5 : R1a
TEM6 : R1a
TEM7 : U4
TEM8 : U (?)
TET1 : I1d
VIN3 : U5a1
VIN8 : J1b1a1
Points of interest:
- U5a is found in all periods. All the Bronze Age samples are U5a1, which I have described as the main Indo-European subclade of U5 (although of Mesolithic Northeast European origin).
- Haplogroup T is oddly absent from the Catacomb samples. T1a, which I have linked to the spread of PIE people, is found in several Yamna samples. Chalcolithic samples only have T2, including T2e (also found in LBK samples from Neolithic Germany).
- J1b1a1, one of the maternal lineages most strongly associated with the original pre-IE R1b people in the Near East, is found in two Catacomb samples.
- Haplogroups I and W, which are both strongly associated with PIE migrations, are indeed found in Bronze Age samples, and W even in a Late Chalcolithic sample.
- Note the absence of haplogroup V, which has been very elusive in ancient samples from all periods.
- The Early Chalcolithic samples look very much like Near Eastern farmers. I would expect that these lineages (H5, H7, T2e) represent the arrival of G2a3, J2b2 and T into the Pontic Steppe from the Carpathians or Balkans.
- The Late Chalcolithic samples look much more native Europeans, and probably represent the descendants of the Mesolithic inhabitants of the steppes (I2a1 and/or R1a), or new immigrants from the north.
- Apart from one U4a1 sample from Yamna in Moldova, U4 is found exclusively in Catacomb samples and at extremely high frequency (28%). This tends to confirm my hypothesis that Yamna was an R1b-dominant culture or mixed R1a-R1b, and that R1a tribes from the north invaded the Pontic Steppe from central European Russia and the Volga-Ural during the Catacomb culture. U4 strongly correlates with R1a and peaks in the Volga-Ural region today.
- Overall, the Yamna samples look quite similar to those from the Corded Ware culture. Therefore there might have been more R1a in the Yamna culture that I expected. In that case, the bulk of R1b would have been in the Maykop culture or in very coastal parts of the Pontic Steppe. I believe that the J1b1a samples (TEM3 and VIN8) are the most reliable proxy for Y-DNA R1b. The samples are from Vinogradnoe, immediately north of Crimea, and Temrta in southern Russia, between the North Caucasus and Kalmykia (only about 250 km from Maykop). TEM3 was not tested for autosomal DNA, but VIN8 had apparently dark skin. However it is one of the three samples derived for the TYR gene.
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