Individual genetic distances were estimated using the allele sharing distance (ASD)
[11 ]. The tree of individuals, based on
the ASD distance, was constructed using the neighbour-joining method [12 (link)] with the Molecular Evolutionary Genetics Analysis
software package (MEGA version 2.1) [13 (link)]. The
tree branching pattern was evaluated by bootstrapping, and was based on 100
replicates. The principal coordinates analysis (PCA) was carried out with NTSYS
software [14 ]. The computer program STRUCTURE
2.0 [15 (link)] was used to infer relative
individual admixture levels in the sample. The analysis was carried out with an
admixture model of K = 3 (three populations), the model previously determined to show
the highest posterior probabilities for these data. A total of 25,000 simulation
iterations were run for the burn-in period and 75,000 additional iterations were run
to get parameter estimates. For estimations of individual admixture in the
African-American sample, we included only the European-American and African-American
subjects and set K = 2 with independent alphas. The average individual admixture in
the African-American sample was 0.25.
Locus-specific branch lengths (LSBLs), x, y and z, were
calculated using pairwise FST distances, dAB, dBC
and dAC, where x = (dAB + dAC -
dBC)/2, y = (dAB, + dBC -
dAC)/2, z = (dAC + dBC - dAB)/2.
A, B and C are the three populations under consideration. Figure1 shows these calculations. LSBL correlations were estimated after
transforming the data to more closely approach normality using the inverse
transformation after adding 0.35 to make each measure positive. Computer simulations
of the coalescent process were performed using Hudson's program, called
ms[16 (link)]. Comparisons between
the real data distributions of LSBL and the simulated results were conducted using
the Kolmogorov-Smirnov (KS) test.
[11 ]. The tree of individuals, based on
the ASD distance, was constructed using the neighbour-joining method [12 (link)] with the Molecular Evolutionary Genetics Analysis
software package (MEGA version 2.1) [13 (link)]. The
tree branching pattern was evaluated by bootstrapping, and was based on 100
replicates. The principal coordinates analysis (PCA) was carried out with NTSYS
software [14 ]. The computer program STRUCTURE
2.0 [15 (link)] was used to infer relative
individual admixture levels in the sample. The analysis was carried out with an
admixture model of K = 3 (three populations), the model previously determined to show
the highest posterior probabilities for these data. A total of 25,000 simulation
iterations were run for the burn-in period and 75,000 additional iterations were run
to get parameter estimates. For estimations of individual admixture in the
African-American sample, we included only the European-American and African-American
subjects and set K = 2 with independent alphas. The average individual admixture in
the African-American sample was 0.25.
Locus-specific branch lengths (LSBLs), x, y and z, were
calculated using pairwise FST distances, dAB, dBC
and dAC, where x = (dAB + dAC -
dBC)/2, y = (dAB, + dBC -
dAC)/2, z = (dAC + dBC - dAB)/2.
A, B and C are the three populations under consideration. Figure
transforming the data to more closely approach normality using the inverse
transformation after adding 0.35 to make each measure positive. Computer simulations
of the coalescent process were performed using Hudson's program, called
ms[16 (link)]. Comparisons between
the real data distributions of LSBL and the simulated results were conducted using
the Kolmogorov-Smirnov (KS) test.
