Fig. 2: Genome contributions to synthetic hybrids.

The numbers and sources of chromosomes for each synthetic hybrid were inferred from sppIDer plots (Supplementary Fig. 3), which were corrected based on flow cytometry ploidy estimations. a The number of chromosomal aberrations was inferred for each synthetic hybrid as new translocation, gain, and loss events not seen in the preceding hybrid (Supplementary Fig. 3). Chromosomal aberrations involving parts of chromosomes were conservatively counted only in cases of clear fusion of entire arms, whereas smaller loss-of-heterozygosity events were not counted. The synthetic hybrids generated from each independent scheme are represented with different shapes. Color points are colored according to the number of species genomes contributing to the strain. A LOESS regression line and the 95% confidence interval of the fit are represented with a discontinuous black color and gray shadow, respectively. b Chromosome content is colored according to the species donor. Mitochondrial inheritance was inferred using mitosppIDer (Supplementary Fig. 4). The numbers of chromosomes for each species are colored according to the left heatmap legend. Incomplete and recombinant mtDNA are colored in gray. Total number of chromosomes is shown in the right part, which is colored according to the right legend. Ploidy estimates based on de novo genome assemblies, which correlates with flow cytometry (Spearman rank-sum test R = 0.88, p value = 7.5 × 10⁻⁸, Supplementary Fig. 5c), are indicated at the right side. Synthetic hybrids are reported in the order constructed (Supplementary Fig. 2). yHRW134 and yHRWh4 are shown multiple times because of their use in multiple crossing schemes. Evolved hybrids are grouped based on the conditions in which they were evolved, and they are colored according to their ancestor hybrid. Red squares highlight chromosomes that were retained or lost in all hybrids evolved in the same condition when compared to their siblings evolved in the other condition. S. cerevisiae chromosome IV, where the xylose utilization genes were inserted, is indicated by the black square. Considerable karyotypic diversity continued to be generated during 80 generations of ALE (Fig. 6), but each evolved strain is easily recognized as more similar to its ancestor six-species hybrid. Source data are provided in the Source Data file and at http://bit.ly/2v1rq1T.