|
|
Post by Admin on Dec 4, 2021 22:49:16 GMT
LYG001.A0101 could be assigned as haplogroup R1b1a2 based on the mutations PF6399:C-
>T, PF6430:T->A, L265:A->G, PF6434:A->G, PF6438:C->T, L150.1:C->T, PF6475:C->A,
CTS8728:C->T, PF6482:A->G, PF6494:G->A, PF6497:C->G, PF6505:G->A, PF6509:A->G.
MK5001 could be assigned as haplogroup L based on the mutations L878: A->G, M61: C->T,
and L855: C->T. This individual also has multiple upstream mutations for haplogroup LT:
CTS753: G->A, L298: T->C, PF5531: C->T, PF5536: C->A, CTS2888: A->G, CTS3648: C-
>T, CTS5175: A->G, and PF5566: G->T.
MK5004 could be assigned as haplogroup L based on the mutations L878: A->G, M185: C->T,
M61: C->T, and L855: C->T. This individual also has multiple upstream mutations for
haplogroup LT: CTS753: G->A, L298: T->C, PF5531: C->T, PF5536: C->A, CTS2888: A->G,
CTS3648: C->T, CTS4783: T->C, and CTS5175: A->G.
MK5009.A0101 could be assigned as R1b1a2 based on the mutations L773: A->G, L482: G-
>A, PF6432: C->A, PF6434: A->G, L150.1: C->T, PF6475: C->A, PF6494: G->A, PF6495:
G->A, and PF6509: A->G.
NV3001 could be assigned as Q1a2 based on the mutations M346: C->G, L56: G->A, and
CTS2656: C->T. This individual also has multiple upstream mutations for haplogroup Q1a:
F1426: C->T, FGC8413: A->T, FGC8415: G->T, CTS2006: C->T, CTS4793: C->G, and
CTS5301: G->A and haplogroup Q1: P36.2: G->T, L232: G->A, and L274: A->G.
OSS002.B0101 could be assigned as haplogroup J based on the mutations F1181: G->C,
CTS5934: C->T, and F3119: C->T.
PG2001 could be assigned as haplogroup R1b1 based on the mutation M415: C->A. This
individual also has one upstream mutation for haplogroup R1b: M343: C->A and multiple
upstream mutations for haplogroup R1: P294: G->C, P231: A->G, P225: G->T, P286: C->T,
and M306: C->A.
PG2004 could be assigned as haplogroup R1b1 based on the mutation L278: C->T (we note
that this mutation might be caused by ancient DNA damage). This individual also has one
upstream mutation for haplogroup R1b: M343: C->A and multiple upstream mutations for
haplogroup R1: P294: G->C, P242: G->A, P231: A->G, P286: C->T.
RK1001.C0101 could be assigned as haplogroup R1b1a2 based on the mutations L773: A->G,
PF6430: T->A, L265: A->G, PF6434: A->G, PF6438: C->T, L150.1: C->T, CTS3575: C->G,
PF6482: A->G, and PF6495: G->A.
RK4001.A0101 could be assigned as haplogroup R1b1a2 based on the mutations PF6434: A-
>G, PF6438: C->T, L150.1: C->T, PF6475: C->A, PF6482: A->G, PF6497: C->G, PF6505: G-
>A, and CTS12478: G->A.
RK4002.B0101 could be assigned as haplogroup R1b1a2 based on the mutations M520: T->A,
PF6430: T->A, L265: A->G, PF6434: A->G, PF6438: C->T, PF6475: C->A, CTS8728: C->T,
PF6482: A->G, PF6494: G->A, PF6495: G->A, PF6497: C->G
SA6003.B0101 could be assigned as haplogroup R1b1a2 based on the mutations L265: A->G,
PF6434: A->G, L150.1: C->T, PF6482: A->G, and PF6495: G->A.
|
|
|
|
Post by Admin on Dec 5, 2021 2:34:57 GMT
SA6004 could be assigned as haplogroup Q1a2 based on the mutations M346: C->G, L56: G-
>A, and CTS2656: C->T. This individual also has one upstream mutation for haplogroup Q1a:
CTS97: T->A, F903: G->C, F1304: G->T, FGC8415: G->T, CTS1845: G->C, CTS2006: C-
>T, CTS4793: C->G, CTS5804: G->A, CTS7611: A->T, M1115: G->A, M1158: C->T,
M1168: G->A, M1169: G->A and haplogroup Q1: P36.2: G->T, L232: G->A.
SA6013.B0101 could be assigned as haplogroup R1 based on the mutations P294: G->C, P225:
G->T, P236: C->G, and M306: C->A.
SIJ002.A0101 could be assigned as haplogroup L based on the mutations L863: T->C, L878:
A->G, M11: A->G, M61: C->T, L855: C->T. This individual also has multiple upstream
mutations for haplogroup LT: CTS753: G->A, L298: T->C, PF5531: C->T, PF5536: C->A,
CTS2888: A->G, and CTS5175: A->G.
VEK007.A0101 could be assigned as haplogroup J based on the mutations CTS687: A->T,
PF4505: T->C, F1167: G->A, FGC3271: G->A, L60: C->T, CTS4204: G->A, F2116: C->G,
CTS5628: C->G, CTS6958: G->A, CTS7738: T->C, PF4575: A->G, F2839: C->T, P209: T-
>C, F2973: C->T, F3138: G->A, PF4595: C->A, YSC0000228: G->T, CTS10858: G->A,
CTS11291: G->T, and CTS11571: C->A.
VEK009.A0101 could be assigned as haplogroup J1 based on the mutation L255: A->C. This
individual also has multiple upstream mutations for haplogroup J: CTS852: G->A, CTS1250:
G->T, PF4513: C->T, CTS2769: T->A, CTS3732: A->G, CTS4349: G->A, CTS7229: C->A,
F2502: G->A, CTS7738: T->C, F4299: T->A, S22619: C->A, F4300: T->A, F3176: T->C, and
CTS11571: C->A.
I2055 could be assigned as haplogroup J based on the mutations PF4513: C->T, L60: C->T,
CTS2769: T->A, F2839: C->T, PF4595: C->A, L778: T->C, CTS11787: G->A, PF4513: C-
>T, L60: C->T, CTS2769: T->A, F2839: C->T, PF4595: C->A, L778: T->C, and CTS11787:
G->A.
I2056 could be assigned as haplogroup J2a based on the mutations L559: A->G and L152: C-
>T. This individual also has multiple upstream mutations for haplogroup J: CTS687: A->T,
CTS852: G->A, PF4505: T->C, CTS1250: G->T, PF4513: C->T, PF4515: G->A, F1167: G-
>A, F1168: G->A, PF4519: C->G, F1381: G->T, PF4521: T->C, PF4524: G->A, FGC3271:
G->A, PF4530: C->T, CTS2042: T->A, L60: C->T, F1826: G->A, CTS3732: A->G, CTS4204:
G->A, F2116: C->G, CTS5628: C->G, CTS5678: A->T, CTS7229: C->A, F2502: G->A,
CTS7832: A->G, PF4572: A->G, PF4575: A->G, F2769: G->C, CTS8974: A->G, F2817: C-
>T, F2839: C->T, CTS9533: C->A, P209: T->C, CTS10446: G->C, F3119: C->T, F4299: T-
>A, S22619: C->A, F4300: T->A, PF4591: C->A, PF4595: C->A, FGC1599: A->T, PF4598:
A->G, F3347: C->T, M304: A->C, CTS11571: C->A, CTS11750: C->T, CTS11787: G->A,
and CTS12047: A->G.
I2051 could be assigned as haplogroup J based on the mutations F1167:G->A, FGC1604:G-
>A, CTS4349:G->A, PF4567:A->C, F2746:G->A, F2769:G->C.
I6266 could be assigned as haplogroup J2a1 based on the mutations L26: T->C and F4326: A-
>G. This individual also has one upstream mutation M410:A->G defining haplogroup J2a and
mutiple upstream mutations for haplogroup J: PF4513:C->T, F1167:G->A, F1181:G->C,
PF4519:C->G, PF4521:T->C, PF4524:G->A, FGC1604:G->A, FGC3271:G->A, PF4530:C-
>T, F1744:G->A, CTS2769:T->A, CTS4204:G->A, F2114:G->A, F2116:C->G, CTS5628:C-
>G, CTS5934:C->T, CTS6958:G->A, CTS7028:T->C, CTS7229:C->A, CTS7483:T->A,
PF4567:A->C, CTS7738:T->C, PF4575:A->G, CTS8974:A->G, CTS9533:C->A, P209:T->C,
CTS10446:G->C, F3119:C->T, PF4591:C->A, F3176:T->C, PF4594:C->A, CTS10858:G->A,
CTS11291:G->T, CTS12047:A->G.
I6268 could be assigned as haplogroup J2a1 based on the mutation L26:T->C. This individual
also has mutiple upstream mutations for haplogroup J: CTS687:A->T, F1181:G->C, PF4519:C-
>G, PF4524:G->A, FGC3271:G->A, F1744:G->A, CTS2769:T->A, CTS3936:G->A,
CTS4204:G->A, CTS5678:A->T, CTS7028:T->C, F2502:G->A, CTS7832:A->G, F2839:C-
>T, CTS9533:C->A, F3119:C->T, CTS11291:G->T, CTS11765:A->T.
I6272 could be assigned as haplogroup G2a2a based on mutations PF3165: C->A and
PF3184:C->T. This individual also has mutiple upstream mutations for haplogroup G2a:
F4086:C->T, Z3240:A->G, F2301:G->A, F2529:A->G, CTS11463:G->A
We were not able to determine the haplogroups of the following samples due to low coverages:
IV3002.A0101, MK5007.B0101, MK5008.B0101, MK5012.A0101, SA6010.A0101,
VEK008.A0101, I1720, I1723, and I6270.
|
|
|
|
Post by Admin on Dec 5, 2021 20:01:24 GMT
Supplementary Note 5 Dating gene flow from Caucasus mountain groups into Steppe Maykop In this section, we estimated admixture time for the observed farmer related ancestry in Steppe Maykop outlier individuals using the linkage disequilibrium (LD)-based admixture inference implemented in ALDER54. We computed weighted LD curves with Steppe Maykop outlier as the test population and Steppe Maykop and Kura_Araxes as references. The average admixture time for Steppe Maykop outlier is about 20 generations ago (about 580 years ago assuming 29 years per generation55). We caution that the date estimates might not reflect the initial farmer related admixture in Steppe Maykop outliers; instead, it is an average date of population mixture. If the admixture did not happen immediately when two populations met, or occurred many times over an extended period, the true start of mixture would be more ancient. ---- fit on data from 0.30 to 50.00 cM (using inter-chrom affine term) ---- d>0.30 decay: 23.34 +/- 70.67 z = 0.33 d>0.30 amp_tot: 0.00012067 +/- 0.00016094 d>0.30 amp_exp: 0.00011854 +/- 0.00016048 z = 0.74 d>0.30 amp_aff: 0.00000427 +/- 0.00000419 ---- fit on data from 0.40 to 50.00 cM (using inter-chrom affine term) ---- d>0.40 decay: 21.04 +/- 9.72 z = 2.17 * d>0.40 amp_tot: 0.00010361 +/- 0.00006259 d>0.40 amp_exp: 0.00010147 +/- 0.00006192 z = 1.64 d>0.40 amp_aff: 0.00000427 +/- 0.00000419 ---- fit on data from 0.50 to 50.00 cM (using inter-chrom affine term) ---- d>0.50 decay: 19.83 +/- 8.26 z = 2.40 * d>0.50 amp_tot: 0.00009353 +/- 0.00005701 d>0.50 amp_exp: 0.00009139 +/- 0.00005643 z = 1.62 d>0.50 amp_aff: 0.00000427 +/- 0.00000419 ---- fit on data from 0.60 to 50.00 cM (using inter-chrom affine term) ---- d>0.60 decay: 21.22 +/- 9.69 z = 2.19 * d>0.60 amp_tot: 0.00010532 +/- 0.00006435 d>0.60 amp_exp: 0.00010319 +/- 0.00006376 z = 1.62 d>0.60 amp_aff: 0.00000427 +/- 0.00000419 ---- fit on data from 0.70 to 50.00 cM (using inter-chrom affine term) ---- d>0.70 decay: 22.82 +/- 94.81 z = 0.24 d>0.70 amp_tot: 0.00011856 +/- 0.00032577 d>0.70 amp_exp: 0.00011643 +/- 0.00032553 z = 0.36 d>0.70 amp_aff: 0.00000427 +/- 0.00000419  |
|
|
|
Post by Admin on Dec 6, 2021 0:12:58 GMT
Supplementary Note 7 Phenotypic variants and marker under selection We also explored a set of SNPs that has been shown to be under selection in West Eurasia over the last 8000 years of human history59 (Supplementary Table 24). We observe an almost complete lack of the derived allele at the LCT locus, which codes for lactase persistence, i.e. the ability to digest milk sugar in adulthood. Only one 4000-year-old individual from the Late North Caucasus site of Kabardinka is heterozygous for the derived allele. The SNPs at SLC24A5 and SLC45A2 are associated with lighter skin pigmentation and HERC2 with lighter eye colour. The great majority of individuals from both main clusters likely had lighter skin colour, while the eye colour varied within each cluster. Interestingly, one of the Steppe Maykop individuals carried the derived allele at the EDAR 370A locus, which was shown to be at high frequency in East Asia thus associated with straighter, thicker hair and shovel-shaped incisors. This finding is consistent with the ancestral East Asian/Siberian affinity shown above.  Supplementary Table 24. Allele information on phenotypic SNPs that thought to be affected by selection. Only high-quality (q>30) bases were counted. rs4988235 on the LCT gene is responsible for lactase persistence in Europe. The SNPs at SLC24A5 and SLC45A2 are responsible for light skin pigmentation. The SNP at EDAR affects tooth morphology and hair thickness. The SNP at HERC2 is the primary determinant of light eye colour in present-day Europeans. We highlight in light blue sites that are likely to be heterozygous, and in red sites that are likely to be homozygous for the derived allele. |
|
|
|
Post by Admin on Dec 6, 2021 21:45:00 GMT
Supplementary Note 6 Admixture Graph modelling In previous analyses, we defined two genetic clusters within the Greater Caucasus region, correlating to the Caucasus groups of the northern foothills and Steppe groups of the bordering steppe regions. In this section, we use the method qpGraph56, as implemented in ADMIXTOOLS57 to test models of possible phylogenetic relationships for the two genetic clusters with reported representatives of ancient West Eurasians. qpGraph assesses the fit of Admixture Graph models to data by computing f2-, f3- and f4- statistics measuring allele sharing among pairs, triples, and quadruples of populations and evaluating fits based on the maximum |Z|-score comparing predicted and observed values of these statistics. We use the newly generated Maykop and Yamnaya_Caucasus data to represent the above two clusters, respectively. We also add Eneolithic_Steppe into the graph as a potential source for the Steppe groups.  We started with a skeleton phylogenetic tree consisting of Mbuti, Loschbour, and MA1 without admixture (Supplementary Figure 11), which could be fitted in the graph without outliers: Supplementary Figure 11. Skeleton Admixture Graph without admixture edges. Fit to genetic data with no f-statistics more than |Z|>3 different between model and expectation. The Z-score of the worst f-statistic (Mbuti, MA1; MA1, Loschbour) = -0.078. The drift along edges (number next to the arrows) is multiplied by 1000. We then added Globular_Amphora as a representative of European farming populations to all possible edges in the graph of Supplementary Figure 11. We obtained one tree topology that fitted with no outliers and one additional admixture event implying that Globular_Amphora derived ancestry from Loschbour and a basal lineage branching off earlier than the split of MA1 and Loschbour (Supplementary Figure 12), which is consistent with a previous study that reported that Early European Farmers (EEF) had basal Eurasian ancestry58. |
|
