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The long‐distance migrations of thousands of bird species and their billions of individuals are feats of astounding physiological specialization and plasticity. Whereas numerous organ systems require modification to achieve successful fueling and navigation capabilities, given their overarching importance for movement and contribution to body mass, skeletal muscles are subject to exceptional performance optimization and anatomical plasticity. To express the appropriate changes throughout the complicated life history of migration, while remaining in synchrony with the environment, skeletal muscles must receive preparatory signals and express transcriptional and biochemical modifications required for full expression of the migratory phenotype. In all likelihood, these muscles must also temporally signal their state and needs to other organ systems. By considering other well‐studied avian skeletal muscle systems, this review explores how endocrine signaling likely impacts skeletal muscles involved in migration and, conversely, how those muscles might relay their condition elsewhere throughout the bird's body. Systems biology offers exceptional modeling for capturing this complex biology. 

Identifying the molecular process of complex trait evolution is a core goal of biology. However, pinpointing the specific context and timing of trait-associated changes within the molecular evolutionary history of an organism remains an elusive goal. We study this topic by exploring the molecular basis of elaborate courtship evolution, which represents an extraordinary example of trait innovation. Within the behaviorally diverse radiation of Central and South American manakin birds, species from two separate lineages beat their wings together using specialized “superfast” muscles to generate a “snap” that helps attract mates. Here, we develop an empirical approach to analyze phylogenetic lineage-specific shifts in gene expression in the key snap-performing muscle and then integrate these findings with comparative transcriptomic sequence analysis. We find that rapid wing displays are associated with changes to a wide range of molecular processes that underlie extreme muscle performance, including changes to calcium trafficking, myocyte homeostasis and metabolism, and hormone action. We furthermore show that these changes occur gradually in a layered manner across the species history, wherein which ancestral genetic changes to many of these molecular systems are built upon by later species-specific shifts that likely finalized the process of display performance adaptation. Our study demonstrates the potential for combining phylogenetic modeling of tissue-specific gene expression shifts with phylogenetic analysis of lineage-specific sequence changes to reveal holistic evolutionary histories of complex traits.