  A major challenge in biology is explaining how novel characters originate,
however, the molecular mechanisms that underlie the emergence of evolutionary
innovations are unclear. Here we show that while gene expression in the uterus
evolves at a slow and relatively constant rate, it has been punctuated by
periods of rapid change associated with the recruitment of thousands of genes
into uterine expression during the evolution of pregnancy in mammals. We found
that numerous genes and signaling pathways essential for the establishment of
pregnancy and maternal-fetal communication evolved uterine expression in
mammals. Remarkably the majority of genes recruited into endometrial expression
have cis-regulatory elements derived from lineage-specific transposons,
suggesting that that bursts of transposition facilitate adaptation and
speciation through genomic and regulatory reorganization.
