Proportion of gene pairs conserved in a comparator versus intergene distance in S. cerevisiae. Profiles of the rate of gene pairs conserved versus their current spacer in S. cerevisiae (red) or in simulants (blue) when comparing S. cerevisiae with two comparator species for (a) C. glabrata and (b) A. gossypii. For the simulations the number of inversions to run was determined by comparing observed synteny conservation rates against inversion number as shown in Figure 1. For our five focal species we also restricted analysis to cases where both of the orthologues of the S. cerevisiae gene pair are on the same chromosome in the comparator species, as this fits better the simulant model and permits higher orthology certainty. Each data point in the real and simulant data represents the proportion of gene pairs from 50 showing conserved synteny, after the data was rank ordered by intergene distance. After considering the first 50 we then considered ranks 2-51, 3-52, and so on. In addition, we also considered other comparators, and a much more distant comparator, C. albicans (Additional data file 1).