Genome shock in a migratory songbird hybrid zone
The genomic shock hypothesis proposes that hybridization destabilizes genome regulation, leading to increased chromatin accessibility and the activation of transposable elements (TEs). While extensively studied in plants, evidence in vertebrates is limited. We tested the genome shock hypothesis in a hybrid zone between two subspecies of Swainson thrush (Catharus ustulatus), integrating data from three molecular dimensions (TE proportions from whole genome sequencing, TE expression from RNA-seq data, and genome accessibility from ATAC-seq data) that were assayed from brain regions during migratory and non-migratory phases. Hybrids exhibit higher genome-wide TE proportions, TE expression, and degrees of open chromatin regions than either parental lineage, providing the first direct evidence of genome shock in a wild avian system. TE expression and chromatin accessibility were positively correlated in both migratory phases, but with opposite patterns in each brain area, indicating environmental and tissue specificity. Our results motivate further investigation into its effects on hybrid fitness, reproductive isolation, and genomic incompatibilities.