Fig. 2.

Performances of single- and trans-species variants of HKA, NCD(0.5), T₁, and T₂. (A–C) Schematic of demographic models relating three species, representing human (species H), chimpanzee (species C), and gorilla (species G), adopted in simulations. (A) All three species maintain constant population size of $N={10}^4$ diploid individuals, with species H diverging from species C 5 million years ago (Ma), and the common ancestor of species H and C diverging from species G 8 Ma. (B) Species H went through a 400-generation population bottleneck with size N_b = 550 diploids 22–30 thousand years ago (ka). (C) Species H doubled its population size to $N_{\mathrm{e}}=2\times {10}^4$ diploids 48 ka. Simulations assumed a generation time of 20 years across the entire phylogeny. (D–F) Powers at a 1% FPR of single- and trans-species variants of HKA, NCD(0.5), T₁, and T₂ to detect balancing selection (s = 0.01 with h = 100) of varying age under (D) constant population size, (E) recent strong population bottleneck, and (F) recent population expansion scenarios. Red vertical dashed lines represent the times at which species H and C split, and at which species G split, respectively.