Result of the joint model best-fitting simulation compared with empirical data. (A) Inter-origin distance distribution in simulated species (blue bars) vs. empirical distribution for the 10 Lachancea species (red diamonds). (B) Origin efficiency distribution in simulated (blue bars) vs. empirical species (red diamonds). The agreement between simulation and experimental data shows that this joint evolutionary model reproduces the typical structural features of a yeast genome. (C) Box plot of the distance from the nearest origin split by evolutionary events, that is, for conserved (dark blue), newly gained (blue), and lost origins (black) for simulated species. (D) Fraction of origins that are nearest to conserved, newly gained, and lost for simulated species compared to the expected result for uncorrelated events. (E) Box plot of efficiency of lost, conserved, and newly gained origins (respectively in black, dark blue, and blue) and their neighbors (gray) in simulated species. (F) The efficiency of all conserved and newly gained origins compared to the ones flanking a lost origin. Braces indicate subsampling. Box plots show the median (bar), 25–75 (box), and 10–90 (whiskers) percentiles. Panels (D–F) show that the model correctly reproduces the correlation between origin birth-death events over evolution and efficiency of the nearest origin. Simulation parameters (see Materials and methods): , , overall birth and death rate , , and rate of origin firing rate reshuffling , where is measured by protein-sequence divergence. Panels (A) and (B) show data from approximately 600,000 simulated origins, while panels (C–F) data from about 100,000 birth and death events and 500,000 conservation events.