A common ancestor similar to the modern Kluyveromyces yeast duplicated its genome (1). Some genes were lost (2). Duplicate genes such as 3 and 13 are in the same relative order. The bottom panel compares the two modern genomes.
[Data from Figure 1, Manolis Kellis, Bruce W. Birren, and Eric S. Lander, “Proof and Evolutionary Analysis of Ancient Genome Duplication in the Yeast Saccharomyces cerevisiae,” Nature 428, April 8, 2004, copyright Nature Publishing Group.]