Caucasus Hunter-Gatherers/CHG: Europe's 4th Ancestral Tribe

Caucasus Hunter-Gatherers/CHG: Europe's 4th Ancestral Tribe May 14, 2021 20:06:21 GMT

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Post by Admin on May 14, 2021 20:06:21 GMT


Supplementary Table 23: Numbers of reads mapped on X chromosome or Y chromosome
versus the autosomes and Y-haplogroup typings.
Nseqs: the total number of reads mapped on the human reference genome.
Sample Nseqs xCov/autCov yCov/autCov Sex Y haplogroup
ARM001.A0101 2809801 0.7581 0.0090 Female -
ARM002.A0101 4192423 0.3632 0.5074 Male G2b
ARM003.A0101 4004409 0.3638 0.5096 Male G2b
AY2001.A0101 9141500 0.7028 0.0103 Female -
AY2003.A0101 6390930 0.6990 0.0101 Female -
BU2001.A0101 839079 0.3700 0.5023 Male R1b1a2a2
GW1001.A0101 3048224 0.3192 0.4830 Male R1b1a2a2
IV3002.A0101 787369 0.3717 0.4531 Male ?
KBD001.A0101 6270235 0.3636 0.5348 Male R1b1a2
KBD001.B0101 7255204 0.3580 0.5005 Male R1b1a2 independent replicate of KBD001.A0101
KBD002.A0101 6414457 0.7109 0.0163 Female -
KDC001.A0101 5303973 0.3572 0.6167 Male J2b
KDC002.A0101 3696144 0.6972 0.0058 Female -
LYG001.A0101 2696989 0.3427 0.4518 Male R1b1a2
MK3003.A0101 2393147 0.7391 0.0061 Female -
MK5001.A0101 2810302 0.3517 0.5076 Male L
MK5001.B0101 1678751 0.3628 0.4801 Male L independent replicate of MK5001.A0101
MK5004.A0101 5088083 0.3487 0.5254 Male L
MK5004.D0101 2229129 0.3657 0.4493 Male L independent replicate of MK5004.A0101
MK5005.C0101 360284 0.7318 0.0100 Female -
MK5007.B0101 3810 0.3649 0.2617 Male ?
MK5008.B0101 160876 0.3858 0.4920 Male ?
MK5009.A0101 1595419 0.3760 0.4413 Male R1b1a2
MK5012.A0101 42251 0.3734 0.3966 Male ?
NV3001.A0101 4792208 0.3529 0.5151 Male Q1a2
NV3001.B0101 1901486 0.3671 0.5310 Male Q1a2 independent replicate of NV3001.A0101
OSS001.A0101 1678590 0.7339 0.0102 Female -
OSS002.B0101 211342 0.4107 0.4484 Male J
PG2001.B0101 4746096 0.3751 0.4840 Male R1b1
PG2001.B0201 3940122 0.3601 0.4985 Male R1b1 independent replicate of PG2001.B0101
PG2002.A0101 970812 0.7579 0.0062 Female -
PG2004.A0101 4990081 0.3631 0.4915 Male R1b1
PG2004.C0101 2876965 0.3619 0.4793 Male R1b1 independent replicate of PG2004.A0101
RK1001.C0101 4945393 0.3177 0.4435 Male R1b1a2
RK1003.C0101 463135 0.7233 0.0087 Female -
RK1007.A0101 509895 0.7375 0.0099 Female -
RK4001.A0101 2513859 0.3525 0.4741 Male R1b1a2
RK4002.B0101 3161001 0.3662 0.4834 Male R1b1a2
SA6001.A0101 6979281 0.6900 0.0144 Female -
SA6002.A0101 5684148 0.6912 0.0101 Female -
SA6003.B0101 1387568 0.3703 0.4389 Male R1b1a2
SA6004.A0101 5436082 0.3511 0.3897 Male Q1a2
SA6004.B0101 1257786 0.3462 0.4854 Male Q1a2 independent replicate of SA6004.A0101
SA6010.A0101 1139408 0.3631 0.4484 Male ?
SA6013.B0101 1753402 0.3723 0.4230 Male R1
SIJ002.A0101 5726979 0.3464 0.5820 Male L
SIJ003.A0101 4934680 0.7279 0.0084 Female -
VEK006.A0101 598647 0.7295 0.0040 Female -
VEK007.A0101 1552864 0.4009 0.4473 Male J
VEK008.A0101 34601 0.4110 0.3429 Male ?
VEK009.A0101 1031812 0.3757 0.4305 Male J1
VJ1001.B0101 2719429 0.7505 0.0049 Female -
VJ1001.D0101 3109023 0.7380 0.0052 Female - independent replicate of VJ1001.B0101
ZO2002.C0101 2191544 0.7108 0.0071 Female -
I1722 658099 0.7132 0.0120 Female -
I2055 543337 0.3606 0.4647 Male J
I2056 4020874 0.4057 0.4768 Male J2a
I1720 134524 0.3870 0.4308 Male ?
I1723 200416 0.3939 0.4823 Male ?
I2051 337887 0.3586 0.4328 Male J
I6266 1974285 0.4160 0.4926 Male J2a1
I6267 537729 0.8006 0.0161 Female -
I6268 1091304 0.4058 0.4845 Male J2a1
I6270 15010 0.4126 0.4548 Male ?
I6272 1513390 0.4148 0.4876 Male G2a2a
I2057 37124 0.7210 0.1235 undetermined intermediate sex ratio

Y chromosome haplogroup determination
For the male individuals, we determined Y-chromosome haplogroups by identifying the most
derived allele upstream and the most ancestral allele downstream in the phylogenetic tree in the
ISOGG version 11.89 (accessed March 31, 2016) (http://www.isogg.org/tree). If the most
derived Y chromosome SNP upstream was a C->T or G->A substitution (susceptible to ancient
DNA damage), we required as least two derived SNPs to assign it to the haplogroup (otherwise,
we assigned it to the upstream haplogroup).

ARM002.A0101 could be assigned as G2b based on Z8017: A->G, M3115: G->T, PF5721: G-
>A, and Z8020: C->T. This individual also has multiple upstream mutations for haplogroup
G2: F744: G->A, PF2787: C->T, Z3100: C->G, M3469: G->T, L89: C->T, M3480: T->A,
F1189: A->G, F1239: C->T, F1294: T->A, M3491: A->G, PF2912: T->G, Z6023: C->T,
CTS1868: G->A, CTS4413: T->C, CTS4703: C->T, CTS10089: G->A, M3579: A->G, F3198:
G->T, M3585: G->A, PF3119: G->T, F3536: C->T, Z6474: T->C.

ARM003.A0101 could be assigned as G2b based on Z8017: A->G and M3145: A->G. This
individual also has multiple upstream mutations for haplogroup G2: F744: G->A, PF2787: C-
>T, Z3060: G->C, PF2792: A->G, PF2797: C->T, M3480: T->A, F1189: A->G, F1239: C->T,
F1294: T->A, F1393: G->A, M3491: A->G, Z6023: C->T, CTS1900: T->A, CTS4136: G->A,
CTS4413: T->C, F2319: A->T, CTS6742: G->C, CTS7662: C->T, CTS10089: G->A, M3579:
A->G, F3198: G->T, M3585: G->A, P287: G->T, F3536: C->T, Z6474: T->C.

BU2001.A0101 could be assigned as R1b1a2a2 based on Z2105: C->A. This individual also
has three upstream mutations for haplogroup R1b1a2: PF6430: T->A, PF6432: C->A, PF6438:
C->T and three upstream mutations for haplogroup R1: P242: G->A, P238: G->A, P236: C-
>G. GW1001.A0101 could be assigned as R1b1a2a2 based on the mutation Z2105: C->A. This
individual also has three upstream mutations for haplogroup R1b1a2: PF6399: C->T, PF6430:
T->A, PF6434: A->G, PF6438: C->T, L150.1: C->T, PF6475: C->A, PF6482: A->G, PF6509:
A->G, CTS11468: T->G.

KBD001 could be assigned as R1b1a2 based on the mutations: PF6399:C->T, M520:T->A,
L773:A->G, PF6430:T->A, L265:A->G, L483:C->T, PF6434:A->G, PF6438:C->T, L150.1:C-
>T, PF6475:C->A, CTS8728:C->T, L500:C->A, PF6482:A->G, PF6495:G->A, PF6497:C-
>G, PF6505:G->A, M269:T->C, CTS12478:G->A. We note that this individual also has a
downstream mutation L23: G->A determining haplogroup R1b1a2a, but this mutation might be
caused by ancient DNA damage.

KDC001.A0101 could be assigned as J2b based on the mutations: L282: C->T, M12: G->T,
M221: G->A, and M314: A->C. 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,
F1167:G->A, F1168:G->A, F1181:G->C, PF4519:C->G, PF4521:T->C, PF4524:G->A,
FGC1604:G->A, FGC3271:G->A, FGC1609:C->G, PF4530:C->T, F1744:G->A, F1826:G-
>A, CTS3872:G->A, CTS4204:G->A, CTS4349:G->A, F2114:G->A, CTS5628:C->G,
CTS5934:C->T, CTS7229:C->A, F2502:G->A, S19861:T->A, CTS7738:T->C, CTS7832:A-
>G, F2769:G->C, F2839:C->T, CTS9877:A->G, P209:T->C, F2973:C->T, CTS10446:G->C,
F3119:C->T, F4299:T->A, S22619:C->A, F4300:T->A, F3138:G->A, PF4591:C->A,
F3176:T->C, PF4594:C->A, PF4595:C->A, FGC1599:A->T, Z7829:G->C, F3347:C->T,
M304:A->C, CTS11291:G->T, L778:T->C, CTS11571:C->A, CTS11750:C->T,
CTS12047:A->G.

Caucasus Hunter-Gatherers/CHG: Europe's 4th Ancestral Tribe May 15, 2021 3:37:25 GMT

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Post by Admin on May 15, 2021 3:37:25 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.