We used a random subset of 1,000 markers to conduct a Bayesian inference of population structure, which revealed a strong peak in ΔK for K = 3 (ΔK for k2 = 84.6, ΔK for k3 = 713.1 and ΔK for k4 = 12.25) largely corresponding to the species H. annuus, H. petiolaris and H. debilis/praecox (Figure 2). We analyzed population structure using three different sets of 1,000 random markers and obtained the same strong clustering results each time. One individual (btm15–2) clearly stood out as an early generation H. debilis-H. annuus hybrid in all runs conducted (Figure 2). We removed this individual from further analyses of genetic, protein coding and gene expression divergence.