Genome reorganization in F 1 hybrids uncovers the role of 1 
 retrotransposons in reproductive isolation 2

Interspecific hybridization leads to new interactions among divergent genomes, revealing the 15
 nature of genetic incompatibilities having accumulated during and after the origin of species. 16
 Conflicts associated with misregulation of transposable elements in hybrids expectedly result 17
 in their activation and genome-wide changes that may be key to species boundaries. 18
 Repetitive genomes of wild wheats have diverged under differential dynamics of specific long 19
 terminal repeat retrotransposons (LTR-RTs), offering unparalleled opportunities to address 20
 the underpinnings of plant genome reorganization by selfish sequences. Using reciprocal F1 21
 hybrids between three Aegilops species, restructuring and epigenetic repatterning was 22
 assessed at random and LTR-RT sequences with Amplified Fragment Length Polymorphism 23
 and Sequence Specific Amplified Polymorphisms as well as their methylation-sensitive 24
 counterparts, respectively. Asymmetrical reorganization of LTR-RT families predicted to 25
 cause conflicting interactions matched differential survival of F1 hybrids. Consistent with the 26
 genome shock model, increasing divergence of merged LTR-RTs yielded higher levels of 27
 changes in corresponding genome fractions and lead to repeated reorganization of LTR-RT 28
 sequences in F1 hybrids. Such non-random reorganization of hybrid genomes is coherent with 29
 the necessary repression of incompatible TE loci in support of hybrid viability and indicates 30
 that TE-driven genomic conflicts may represent an overlooked factor supporting reproductive 31
 isolation. 32