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Chunk #73 — Methods — Evolutionary genetics of individuals with diverse ancestry — Demographic estimation under selection at linked sites

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Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program.
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We performed demographic inference with the moments105 program by fitting a model of exponential growth with three parameters (NEur0, NEur, TEur) to the site-frequency spectrum. This included two free parameters: the starting time of exponential growth (TEur) and the ending population size after growth (NEur). The ancestral size parameter (that is, the population size when growth begins), NEur0, was kept constant in our model such that the relative starting size of the population was always 1. We applied the inference procedure to either fourfold degenerate sites or sites with B ≥ 0.994. The site frequency spectrum used for inference was unfolded and based on the polarization step described above. The inference procedure was fit using sample sizes (2N) of 1,000, 2,000, 3,000, 4,000 and 4,832 chromosomes. To convert the scaled genetic parameters output by the inference procedure to physical units, we used the resulting theta (also inferred by moments) and a mutation rate106 of 1.66 × 10−8 to generate corresponding effective population sizes (Ne). To convert generations to years, we assumed a generation time of 25 years. The 95% confidence