Fig 2. Coancestry matrices of simulations.

Both panels have n = 1000 individuals along both axes, K = 10 subpopulations (final or intermediate), and F_ST = 0.1. Color corresponds to ${\theta }_{jk}^T$ between individuals j and k (equal to ${\phi }_{jk}^T$ off-diagonal, $f_j^T$ along the diagonal). (A) The independent subpopulations model has ${\theta }_{jk}^T=0$ between subpopulations, and varying ${\theta }_{jj}^T$ per subpopulation, resulting in a block-diagonal coancestry matrix. (B) Our admixture scenario models a 1D geography with extensive admixture and intermediate subpopulation differentiation that increases with distance, resulting in a smooth coancestry matrix with no independent subpopulations (no ${\theta }_{jk}^T=0$ between blocks). Individuals are ordered along each axis by geographical position.