Table 2.
Y Chromosome Haplogroup Frequencies and Diversity Indices Observed in the South African Coloured Population
| Y-Chromosome Hga | nb | Percent | kc | Hg D (SD)d | Ht D (SD)e | Pi (SD)f | |||
|---|---|---|---|---|---|---|---|---|---|
| Sub-Saharan African | |||||||||
| Total | 103 | 45.18 | 78 | 0.68 | (0.04) | 0.99 | (0.00) | 7.43 | (3.50) |
| E-M2 | 55 | 24.12 | 43 | 0.99 | (0.01) | 5.05 | (2.48) | ||
| E-P68∗ | 13 | 5.70 | 9 | 0.92 | (0.06) | 2.83 | (1.59) | ||
| A-M51 | 12 | 5.26 | 8 | 0.94 | (0.05) | 6.97 | (3.52) | ||
| B-M150∗ | 11 | 4.82 | 8 | 0.89 | (0.09) | 2.18 | (1.30) | ||
| E-M35 (xM78, M81, M123, M281) | 8 | 3.51 | 6 | 0.93 | (0.08) | 3.78 | (2.13) | ||
| B-M112 | 3 | 1.32 | 3 | 1.00 | (0.27) | 9.00 | (5.72) | ||
| E-M123∗ | 1 | 0.44 | 1 | … | … | … | … | ||
| West Eurasian/European | |||||||||
| Total | 86 | 37.72 | 67 | 0.70 | (0.04) | 0.99 | (0.00) | 8.44 | (3.94) |
| R-M343 | 41 | 17.98 | 30 | 0.98 | (0.01) | 4.97 | (2.46) | ||
| I-M170 | 20 | 8.77 | 17 | 0.99 | (0.02) | 7.39 | (3.61) | ||
| R-M17g | 12 | 5.26 | 10 | 0.97 | (0.04) | 3.63 | (1.98) | ||
| E-M78 | 5 | 2.19 | 5 | 1.00 | (0.13) | 4.10 | (2.45) | ||
| T-M70 | 4 | 1.75 | 1 | … | … | … | … | ||
| G-M201 | 2 | 0.88 | 2 | 1.00 | (0.50) | 7.00 | (5.29) | ||
| J-M304 | 2 | 0.88 | 2 | 1.00 | (0.50) | 6.00 | (4.58) | ||
| South/southeast Asian | |||||||||
| Total | 39 | 17.11 | 31 | 0.81 | (0.04) | 0.98 | (0.01) | 8.80 | (4.15) |
| F-M89 (xM201, M69, M170, M304, M9) | 14 | 6.14 | 13 | 0.99 | (0.03) | 8.31 | (4.09) | ||
| O-M122 | 8 | 3.51 | 5 | 0.79 | (0.15) | 2.61 | (1.55) | ||
| H-M69 | 5 | 2.19 | 3 | 0.83 | (0.22) | 6.33 | (3.80) | ||
| O-M119 | 4 | 1.75 | 2 | 0.50 | (0.26) | 1.00 | (0.82) | ||
| R-M124 | 3 | 1.32 | 3 | 1.00 | (0.27) | 6.33 | (4.12) | ||
| K-M9 (XM20, M186, LLY22 g, M175, M45, M70) | 3 | 1.32 | 3 | 1.00 | (0.27) | 6.67 | (4.32) | ||
| O-M95 | 2 | 0.88 | 2 | 1.00 | (0.50) | 8.00 | (6.00) | ||
Note: Table S1 provides the full haplogroup and haplotype (STR) dataset.
a
Khoisan-specific Hg is in italics; pan-African Hgs are underlined; Bantu-specific Hgs are marked with an asterisk. We followed the nomenclature conventions recommended by the Y Chromosome Consortium.47
b
Number of individuals.
c
Number of observed STR haplotypes.
d
Gene diversity based on Hg profiles (Hg D) and standard deviation (SD).
e
Gene diversity based on STR haplotypes (Ht D) and standard deviation (SD).
f
Mean number of pairwise differences (Pi) and standard deviation (SD).
g
Hg R-M17 can also be of Indian origin.