Current models of developmental evolution suggest changes in gene regulation underlie the evolution of morphology. Despite the fact that protein complexes regulate gene expression, the evolution of regulatory protein complexes is rarely studied. Here, we investigate the evolution of a protein-protein interaction (PPI) between Homeobox A11 (HoxA11) and Forkhead box 01A (Foxo1a). Using extant and "resurrected" ancestral proteins, we show that the physical interaction between HoxA11 and Foxo1a originated in the mammalian stem lineage. Functional divergence tests and coimmunoprecipitation with heterologous protein pairs indicate that the evolution of interaction was attributable to changes in HoxA11, and deletion studies demonstrate that the interaction interface is located in the homeodomain region of HoxA11. However, there are no changes in amino acid sequence in the homeodomain region during this time period, indicating that the origin of the derived PPI was attributable to changes outside the binding interface. We infer that the amino acid substitutions in HoxA11 altered Foxo1a's access to the conserved binding interface at the HoxA11 homeodomain. We also found an expansion in the number of paired Hox/Fox binding sites in the genomes of mammalian lineage species suggesting the complex has a biological function. Our data indicate that the physical interaction between HoxA11 and Foxo1a evolved through noninterface changes that facilitate the PPI, which prevents inappropriate interactions, rather than through the evolution of a novel binding interface. We speculate that evolutionary changes of intramolecular regulation have limited pleiotropic effects compared with changes to interaction domains themselves.protein-protein interaction evolution | transcription factor evolution C hanges in gene regulation are the driving force in the origin and evolution of novel phenotypes. Gene expression is coordinated by the formation of multiprotein complexes that bind to cis-regulatory promoter and enhancer regions for target genes and activate or repress transcription in a signal-dependent fashion (1-3). There is strong evidence that changes in both cisregulatory elements and regulatory proteins, such as transcription factors, have led to gene regulatory evolution (4-12). However, the mechanisms by which transcription factor evolution affects gene regulation are poorly understood. For example, it has been suggested that the evolution of novel protein-protein interactions (PPIs), posttranslational modifications, and DNA-and ligandbinding specificities may all contribute to the origin of regulatory activities in transcription factors; however, to date, few studies have carefully dissected potential mechanisms.Here, we address this question by investigating the evolution of the physical interaction between two transcription factors, Homeobox A11 (HoxA11) and Forkhead box 01A (Foxo1a), which play a major role in regulating gene expression in endometrial stromal cells during pregnancy in placental mammals (8,13). By examining the a...