Three independent interspecific hybridization events. (A) Three distinct clusters of genomic copies with high genetic variation. A principal component analysis shows that the genomic copies with high genetic variation to the reference genome of strains in the subpopulations teq/EtOH, beer, and wine 1 are not only different to the genomic copy with low genetic variation but are also genetically distinct between subpopulations (based on 24,110 genome-wide distributed SNPs). (B) Phylogenetic relationship from reads with low genetic variation to the reference genome. The genomic copies with low genetic variation are different between the six subpopulations teq/EtOH, beer, wine 1–3, and kombucha, which group according to their ecological origin (based on 24,110 genome-wide distributed SNPs). (C–E) Pairwise genetic diversity between genomic copies from imputed whole-genome sequences. (C) (Left [High*High]) Pairwise comparison of the genomic copies with high levels of intra-genomic variation between strains of the same subpopulations (single-colored dots) show a genetic diversity of <1% (average of 0.13%). Between strains from different subpopulations (two-colored dots indicate the subpopulation dependency of the compared strains), this diversity varies between 1.76% and 3.05%. (Middle [High*Low]) The genetic distance between the genomic copies with low and high levels of variation, irrespective if it is within the same or between strains, is on average 2.92% (two-colored dots indicate the subpopulation dependency of the compared strains). The strain III_F09_YJS8068 is an outlier (black triangle) as it appears to be an admixed diploid with only 1.1% divergence between the highly and lowly diverged parts of its genome. (Right [Low*Low]) Genetic distances between genomic copies of low intra-genomic variation is generally below (0.9%) between strains of the same or different subpopulations. The admixed strain III_F09_YJS8068 is the exception, because it also has the highest variation between the low intra-genomic regions of its genome and the low intra-genomic copies of other strains (>2%). (D) Heatmap showing the genetic distance between genomic copies of 40 polyploid individuals. The only strains whose genomic copies (low intra-genomic variation and high intra-genomic variation) are similar is the admixed III_F09_YJS8068 (black triangle). Here, both genomic copies cluster together with all other genomic copies of high intra-genomic variation. (E) Acquired genomic copy of unknown origin. The genomic copies with low genetic variation were assigned as the primary genomic copies present in all individuals (2n-4n), whereas the genomic copies with high genetic variation were assigned as acquired genomic copies, only present in 40 polyploids of the subpopulations teq/EtOH, beer, and wine 1. Pairwise genetic analysis with the primary genome of the beer subpopulation as a reference shows a clear gap between the genetic variation that defines the primary and the acquired genome. The primary genome of the beer subpopulation is similarly distant to its own acquired genomic copy as well as to the acquired genomic copies of the other two polyploid groups wine 1 and teq/EtOH. The two genetic clusters beyond the 0.9% for the teq/EtOH do not only comprise the pairwise comparison with the acquired genomic copies. The dotted rectangle corresponds to comparisons with the admixed diploid, for which both copies are equally distinct. Genetic distances were calculated pairwise per chromosome and then average per genome (JC69).
