Unraveling the molecular etiology of a novel phenotype is still a major challenge. Mammalian pregnancy, a novel phenotype, preserves its stepwise evolution in extant species, which gives us additional tools to use to begin to unravel its evolution. Within this thesis, the evolution of three components of pregnancy are explored- the regulation of TAP2 expression, the regulation of HLA-F expression, and the possible role of transposable elements in rewiring the regulatory networks underlying major gene expression shifts at the maternal-fetal interface.