Figure 2. Long, high-frequency West African ancestry tracts span the DARC locus in Santiago.

(A) The distribution of West African (purple) and European (green) ancestry tract lengths spanning the DARC locus (dashed line). Each horizontal line represents a single chromosome in the population (n = 343, one chromosome was excluded due to having unknown ancestry at the DARC locus). (B) Decay in Ancestry Tract (DAT) as function of absolute distance from the Duffy-null allele for West African (purple) and European (green) ancestry tracts. (C) Mean standardized integrated DAT (iDAT) score for 20 Mb sliding windows (step size = 1 Mb), using standardized iDAT for 10,000 random positions across the genome. Horizontal solid gray line indicates mean windowed standardized iDAT score (−0.196), and horizontal dashed gray lines indicate three standard deviations from the mean windowed score. The red dot is the most extreme windowed standardized iDAT score (−2.602), indicative of a larger area under the curve for West African DAT compared to European DAT. This 20 Mb window contains the Duffy-null SNP.

Figure 2—figure supplement 1. Mean standardized integrated Decay in Ancestry Tract (iDAT) score for 20 Mb sliding windows (step size = 1 Mb), using standardized iDAT for 10,000 random positions across the genome for (A) Fogo and (B) the Northwest Cluster.

Solid gray lines indicate mean windowed standardized iDAT score for each island (Fogo, 0.006; NW Cluster, −0.024) and dashed gray lines indicate three standard deviations from the mean. Vertical dashed red lines indicate the DARC locus, which is not an outlier for either Fogo or the NW Cluster.

Figure 2—figure supplement 2. Density distributions for five ancestry-based statistics under eight neutral models.

Summary statistics were calculated from a random sample of 172 individuals from each simulated population, matching the number of individuals from Santiago included in our analyses. High population size models correspond to initial N = 10,000, low population size (high drift) models correspond to initial N = 1000. Exponential growth model corresponds to a rate of 0.05 per generation. Continuous migration refers to 1% total new migrants each generation, at the same proportions as initial admixture contributions for each source population. Vertical red line represents each measure’s observed value for Santiago.

Figure 2—figure supplement 3. Density distributions for five ancestry-based statistics under simulations using different genetic maps.

Simulations shown assumed a single pulse of admixture with exponential growth at a rate of 0.05 per generation and an initial population size of N = 10,000. Initial admixture contributions were drawn from a uniform distribution from 0.65 to 0.75. Summary statistics were calculated from a random sample of 172 individuals from each simulated population, matching the number of individuals from Santiago included in our analyses. Genetic maps correspond to the population-averaged IMPUTE2 map, Iberian Population in Spain (IBS)-specific genetic map, Gambian in Western Division (GWD)-specific genetic map, and African American (AA)-specific genetic map. Vertical red line represents each measure’s observed value for Santiago.

Figure 2—figure supplement 4. Performance of integrated Decay in Ancestry Tract (iDAT) under various scenarios.

Each plot corresponds to number of generations since admixture (10 – left; 100 – middle; 1000 – right). Line and point colors correspond to source population one admixture contribution at ${\displaystyle m=0.1}$ (gray), ${\displaystyle m=0.5}$ (yellow), and ${\displaystyle m=0.9}$ (blue). Within each plot, the x-axis shows selection strength for the simulated variant at the Duffy-null position, and the y-axis shows the proportion of Duffy-null iDAT values from the selection simulations that are in the bottom fifth percentile of the simulated neutral Duffy-null iDAT distribution. Notably, iDAT cannot be calculated for variants that are fixed in the population, as was the case for many simulations of older admixture (100 or 1000 generations) and high admixture proportion (m = 0.9) and/or stronger selection. This is reflected in the statistic’s performance under these scenarios.

Figure 2—figure supplement 5. Performance of integrated Decay in Ancestry Tract (iDAT) for various chromosome sizes and cut-off values.

Line and point colors correspond to simulated human chromosome and corresponding size (chr 1 – green; chr 7 – blue; chr 15 – yellow; chr 22 – gray). X-axis shows DAT cut-off values, and y-axis shows proportion of iDAT values at the simulated variant under selection that are in the bottom fifth percentile of simulated neutral iDAT values.