Centromeres evolve progressively through selection at the kinetochore interface

During mitosis, stable but dynamic interactions between the centromere DNA and kinetochore complex enable accurate and efficient chromosome segregation. Even though many proteins of the kinetochore are highly conserved, centromeres are among the fastest evolving regions within a genome, showing extensive variation even on short evolutionary timescales. Here, we sought to understand how new types of centromeres emerge and reach fixation by mapping centromere evolution across 138 budding yeast species and over 2,500 natural strain isolates. We show that new centromeres spread progressively via drift and subsequent selection, and that the kinetochore interface, which is evolving slowly in relative terms, determines which new centromere variants are tolerated. Together, our findings provide insight into the evolutionary constraints and trajectories shaping centromere evolution.