Fig. 1

Illustration of the CEGA method. A Parameters of the CEGA model. Global parameters: divergence time \({T}_{d}\), effective population sizes of the two differentiated species \({N}_{1}\) and \({N}_{2}\) and of the common ancestor \({N}_{0}\). Locus-specific parameters: scaling coefficients \({\lambda }_{1}^{l}\) and \({\lambda }_{2}^{l}\) of \({N}_{1}\) and \({N}_{2}\). B Four locus-specific summary statistics of the observed data, \({S}_{1}\), \({S}_{2}\), \({S}_{12}\), and \(D\). C Examples of gene genealogies of samples under positive selection (red) and balancing selection (blue). The genealogies were constructed from simulated data using MEGA (v. 11)