While we identified many novel lineages that are hybrids between major groups present in our study, it is likely that even with whole-genome variation data we are missing other admixture events especially within groups: This is because admixture analysis is most suited to identify admixed samples between the given K groups, and heterozygosities are most prominent when hybridization occurs between genetically diverse strains. All of our known hybrid populations had elevated levels of heterozygosity, but group Ldon3 was highly heterozygous without distinct genomic patterns of hybridisation (Figure 3A). Clear genomic patterns of hybridisation can be undetectable when hybridisation occurs frequently between closely related strains. This might be the case for the Ldon3 group and is also supported by a steep decline of LD with genomic distance (Figure 5) and the mixed distribution of isolate specific haplotypes within the Ldon3 group (Figure 4—figure supplement 9B–D). However, while we don’t have direct proof of hybridisation in the Ldon3 group, the generality of the relationship between heterozygosity and hybrid origin remains unclear.