Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data
(A) AFS for the YRI, CEU, and CHB populations. The color scale is as in (C). (B) Illustration of the model we fit, with the 14 free parameters labeled. (C) Marginal spectra for each pair of populations. The top row is the data, and the second is the maximum-likelihood model. The third row shows the Anscombe residuals  between model and data. Red or blue residuals indicate that the model predicts too many or too few alleles in a given cell, respectively. (D) The observed decay of linkage disequilibrium (black lines) is qualitatively well-matched by our simulated data sets (colored lines). (E) Goodness-of-fit tests based on the likelihood and Pearson's statistic both indicate that our model is a reasonable, though incomplete description of the data. In both plots, the red line results from fitting the real data and the histogram from fits to simulated data. Poorer fits lie to the right (lower and higher ). (F) The improvement in likelihood from including contemporary migration in the real data fit (red line) is much greater than expected from fits to simulated data generated without contemporary migration (histogram). This indicates that the data contain a strong signal of contemporary migration.