These networks form adaptive topologies, evolving as:
Mutations accumulate (local rewiring),
Selective pressures filter out non-functional variants (topological pruning),
Rare beneficial variants emerge and replicate (network amplification).
This dynamic reflects adaptive walks on fitness landscapes, where topological features---such as shortest paths, basin depths, and network modularity---correspond to key evolutionary concepts like accessibility, robustness, and evolvability.
To quantify these systems:
Betweenness centrality helps identify evolutionary "gateways" (i.e., critical mutational intermediates),
Community detection reveals clusters of functionally similar mutants,
Percolation thresholds identify the emergence of large-scale functional families.
These structures can also capture neutral networks, where many mutations have negligible effects on fitness but set the stage for future innovation---a concept central to molecular evolution and neutral theory.
3. Adaptive Topology as a Bridge Between Folding and Evolution
