RT Journal Article SR Electronic T1 The role of chromosomal inversions in speciation JF bioRxiv FD Cold Spring Harbor Laboratory SP 211771 DO 10.1101/211771 A1 Z.L. Fuller A1 C.J. Leonard A1 R.E. Young A1 S.W. Schaeffer A1 N Phadnis YR 2017 UL http://biorxiv.org/content/early/2017/11/24/211771.abstract AB The chromosomal inversions of D. persimilis and D. pseudoobscura have deeply influenced our understanding of the evolutionary forces that shape natural variation, speciation, and selfish chromosome dynamics. Here, we perform a comprehensive reconstruction of the evolutionary histories of the chromosomal inversions in these species. We provide a solution to the puzzling origins of the selfish Sex-Ratio chromosome in D. persimilis and show that this Sex-Ratio chromosome directly descends from an ancestrally-arranged chromosome. Our results further show that all fixed inversions between D. persimilis and D. pseudoobscura were segregating in the ancestral population long before speciation, and that the genes contributing to reproductive barriers between these species must have evolved within them afterwards. We propose a new model for the role of chromosomal inversions in speciation and suggest that higher levels of divergence and an association with hybrid incompatibilities are emergent properties of ancestrally segregating inversions. These findings force a reconsideration of the role of chromosomal inversions in speciation, not as protectors of existing hybrid incompatibility alleles, but as fertile grounds for their formation.