Fig. 1

Illustration of the eSMC model. A The eSMC using a Pairwise Sequentially Markovian Coalescent model where the observed states are the sequence heterozygosity and the hidden states are the discrete TMRCA. The emission probability and the transition probability is calculated by considering the admixture time \(t_a\) of the populations. The brown dots on the on the curve represents TMRCA states after the admixture events, and the blue dots on the curve represents TMRCA states before the admixture event. The P1 and P2 represents the two admixed populations. B We applied the eMSC method on a 300 kbp diploid genome simulated by msHOT. The black curve indicate the estimated TMRCA (hidden state) along the genome. The heatmap is the inferred TMRCA probability at each loci with the observed sequence. The estimated admixture time is shown as orange dash line on the heatmap. The red stripes at the simulated sequence indicate the heterozygote positions