Chromosomal Fusions Promote Speciation in Subterranean Blind Mole Rats

The genomic mechanisms underlying large-scale chromosomal rearrangements and their evolutionary consequences remain poorly understood. Here, we generated chromosome-level genomes for two sister species pairs of blind mole rats that differ in chromosome numbers. We identified five chromosome fusions during the divergence from a common ancestor (2n = 60). Three shared fusions gave rise to the Spalax galili (2n = 52)-S. golani (2n = 54) clade and accompanied its divergence from the S. carmeli (2n = 58)-S. judaei (2n = 60) clade. Both S. galili and S. carmeli further underwent an independent fusion. These fusions, facilitated by repetitive elements, were associated with changes in three-dimensional genome architecture. Notably, we found reduced gene flow near fusion points. Chromosomal fusions correlated with signatures of selection and may have become fixed through centromeric repeat expansion. Together, these findings provide a genome-wide framework for investigating how chromosomal fusions relate to genome organization and lineage divergence.