Post by Admin on Feb 19, 2022 20:03:07 GMT
S5.11 Sex bias in the spread of Steppe ancestry into South Asia
Taking advantage of our large sample sizes, we tested if the admixture of
Central_Steppe_MLBA ancestry with Indus_Periphery_Pool ancestry that formed the Swat
Valley Late Bronze-Iron Age (SPGT) group was sex-biased, and then tested whether the
admixture of Central_Steppe_MLBA into the ancestors of present-day South Asians was sexbiased.
We began by using qpAdm to estimate the proportion of Central_Steppe_MLBA ancestry in
the SPGT both on the autosomes and on chromosome X. Under the assumption that the
admixture was driven by equal proportions of Central_Steppe_MLBA individuals from each
sex, the proportions on the autosomes (equally reflecting male and female demographic
history) should be consistent with those on chromosome X (primarily reflecting female
history). Table S 90 shows no significant difference between these two compartments of the
genome although standard errors of the X chromosome estimates are so large that the failure
to detect a significant difference does not exclude the possibility of substantial bias.
Indus_Periphery_Pool Central_Steppe_MLBA Standard Error
Autosomes 0.806 0.194 0.009
X 0.850 0.150 0.051
Table S 90 SPGT estimates of Indus_Periphery_Pool and Central_Steppe_MLBA
ancestries on chromosome X and on the autosomes along with the standard error.
We also computed estimates of Steppe pastoralist-related ancestry on the Y chromosome,
taking advantage of the extremely high (100%) frequency of the R1a haplogroup in the
Central_Steppe_MLBA individuals and its complete absence in BA Turan. This nearly fixed
difference in Y chromosome haplogroup frequencies allows us to treat the proportion of R1a
chromosomes as an estimate of the proportion of entirely male-lineage ancestry in the SPGT
from the Central_Steppe_MLBA. We observe only 2 R1a Y chromosomes among the 44
SPGT males in whom we could confidently determine a Y chromosome, corresponding to a
ninety-five percent binomial confidence interval of 0.4-16% for the Y chromosome ancestry
proportions derived from Central_Steppe_MLBA. In comparison, the ninety-five percent
confidence interval for the estimate on the autosomes is 18-21%. The ninety-five percent
confidence intervals are larger on the autosomes than on chromosome Y and do not overlap,
thereby showing that while the X-chromosome estimates are too noisy to be useful here, the
admixture into the SPGT was definitively female-biased.
We also examined if we could detect sex bias on the Modern Indian Cline, and here detected
the reverse pattern. We began by pooling 4 South Asian populations (GIH, ITU, STU and
PJL) from the 1000 Genomes Project for this analysis (76), and computed ancestry
proportions on chromosome X and the autosomes as before. The results do not show any
significant difference, although the data are also consistent with a substantial difference given
the large standard errors on chromosome X (Table S 91).
AHG Indus_Periphery_Pool Central_Steppe_MLBA
Central_Steppe_MLBA
standard error
Autosomes 0.293 0.591 0.116 0.011
X 0.34 0.523 0.137 0.052
Table S 91 Proportions of AHG, Indus_Periphery_Pool and Central_Steppe_MLBA
ancestries on chromosome X and on the autosomes along with the standard error of the
estimates for Central_Steppe_MLBA for the 1000 Genomes Project South Asians.
Using previously reported calls on 1000 Genomes Project Y chromosomes (223), we observe
that 62 out of the 221 South Asian males have an R1a Y chromosome corresponding to a
ninety-five percent binomial confidence interval of 22-34% for Steppe MLBA ancestry on
the entirely male line, which is significantly higher than the ninety-five percent confidence
interval of 9-14% on the autosomes in the same set of individuals. These results shows the
process of admixture of Central_Steppe_MLBA into the ancestors of the ANI was malebiased, and reveal that the directionality of sex bias was opposite to the pattern observed for the contribution of Central_Steppe_MLBA to SPGT.
Taking advantage of our large sample sizes, we tested if the admixture of
Central_Steppe_MLBA ancestry with Indus_Periphery_Pool ancestry that formed the Swat
Valley Late Bronze-Iron Age (SPGT) group was sex-biased, and then tested whether the
admixture of Central_Steppe_MLBA into the ancestors of present-day South Asians was sexbiased.
We began by using qpAdm to estimate the proportion of Central_Steppe_MLBA ancestry in
the SPGT both on the autosomes and on chromosome X. Under the assumption that the
admixture was driven by equal proportions of Central_Steppe_MLBA individuals from each
sex, the proportions on the autosomes (equally reflecting male and female demographic
history) should be consistent with those on chromosome X (primarily reflecting female
history). Table S 90 shows no significant difference between these two compartments of the
genome although standard errors of the X chromosome estimates are so large that the failure
to detect a significant difference does not exclude the possibility of substantial bias.
Indus_Periphery_Pool Central_Steppe_MLBA Standard Error
Autosomes 0.806 0.194 0.009
X 0.850 0.150 0.051
Table S 90 SPGT estimates of Indus_Periphery_Pool and Central_Steppe_MLBA
ancestries on chromosome X and on the autosomes along with the standard error.
We also computed estimates of Steppe pastoralist-related ancestry on the Y chromosome,
taking advantage of the extremely high (100%) frequency of the R1a haplogroup in the
Central_Steppe_MLBA individuals and its complete absence in BA Turan. This nearly fixed
difference in Y chromosome haplogroup frequencies allows us to treat the proportion of R1a
chromosomes as an estimate of the proportion of entirely male-lineage ancestry in the SPGT
from the Central_Steppe_MLBA. We observe only 2 R1a Y chromosomes among the 44
SPGT males in whom we could confidently determine a Y chromosome, corresponding to a
ninety-five percent binomial confidence interval of 0.4-16% for the Y chromosome ancestry
proportions derived from Central_Steppe_MLBA. In comparison, the ninety-five percent
confidence interval for the estimate on the autosomes is 18-21%. The ninety-five percent
confidence intervals are larger on the autosomes than on chromosome Y and do not overlap,
thereby showing that while the X-chromosome estimates are too noisy to be useful here, the
admixture into the SPGT was definitively female-biased.
We also examined if we could detect sex bias on the Modern Indian Cline, and here detected
the reverse pattern. We began by pooling 4 South Asian populations (GIH, ITU, STU and
PJL) from the 1000 Genomes Project for this analysis (76), and computed ancestry
proportions on chromosome X and the autosomes as before. The results do not show any
significant difference, although the data are also consistent with a substantial difference given
the large standard errors on chromosome X (Table S 91).
AHG Indus_Periphery_Pool Central_Steppe_MLBA
Central_Steppe_MLBA
standard error
Autosomes 0.293 0.591 0.116 0.011
X 0.34 0.523 0.137 0.052
Table S 91 Proportions of AHG, Indus_Periphery_Pool and Central_Steppe_MLBA
ancestries on chromosome X and on the autosomes along with the standard error of the
estimates for Central_Steppe_MLBA for the 1000 Genomes Project South Asians.
Using previously reported calls on 1000 Genomes Project Y chromosomes (223), we observe
that 62 out of the 221 South Asian males have an R1a Y chromosome corresponding to a
ninety-five percent binomial confidence interval of 22-34% for Steppe MLBA ancestry on
the entirely male line, which is significantly higher than the ninety-five percent confidence
interval of 9-14% on the autosomes in the same set of individuals. These results shows the
process of admixture of Central_Steppe_MLBA into the ancestors of the ANI was malebiased, and reveal that the directionality of sex bias was opposite to the pattern observed for the contribution of Central_Steppe_MLBA to SPGT.
