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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.
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This content will become publicly available on April 11, 2026
Deep-time gene expression shift reveals an ancient change in avian muscle phenotypes
Gene duplication is an important process of molecular evolutionary change, though identifying these events and their functional implications remains challenging. Studies on gene duplication more often focus on the presence of paralogous genes within the genomes and less frequently explore shifts in expression. We investigated the evolutionary history of calsequestrin (CASQ), a crucial calcium-binding protein in the junctional sarcoplasmic reticulum of muscle tissues. CASQ exists in jawed vertebrates as subfunctionalized paralogs CASQ1 and CASQ2 expressed primarily in skeletal and cardiac muscles, respectively. We used an enhanced sequence dataset to support initial duplication of CASQl in a jawed fish ancestor prior to the divergence of cartilaginous fishes. Surprisingly, we find CASQ2 is the predominant skeletal muscle paralog in birds, while CASQ1 is either absent or effectively nonfunctional. Changes in the amino acid composition and electronegativity of avian CASQ2 suggest enhancement to calcium-binding properties that preceded the loss of CASQ1. We identify this phenomenon as CASQ2 “synfunctionalization,” where one paralog functionally replaces another. While additional studies are needed to fully understand the dynamics of CASQ1 and CASQ2 in bird muscles, the long and consistent history of CASQ subfunctions outside of birds indicate a substantial evolutionary pressure on calcium-cycling processes in muscle tissues, likely connected to increased avian cardiovascular and metabolic demands. Our study provides an important insight into the molecular evolution of birds and shows how gene expression patterns can be comparatively studied across phylum-scale deep time to reveal key evolutionary events
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- PAR ID:
- 10632216
- Editor(s):
- Braasch, Ingo
- Publisher / Repository:
- Public Library of Science
- Date Published:
- Journal Name:
- PLOS Genetics
- Volume:
- 21
- Issue:
- 4
- ISSN:
- 1553-7404
- Page Range / eLocation ID:
- e1011663
- Subject(s) / Keyword(s):
- calsequestrin vertebrates physiology skeletal muscles cardiac muscles evolution molecular evolution gene family synfunctionalization calcium neofunctionalization subfunctionalization
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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