Does fitness increase in Darwinian evolution?

Evolution is a quest for innovation. Organisms adapt to changing natural selection by evolving new phenotypes. Here we develop a nonequilibrium theory of molecular evolution, which extends the static concept of fitness landscapes to dynamic fitness seascapes. The theory shows that adaptive evolution, characterized by surplus of beneficial substitutions over deleterious ones, is a generic state of natural populations. We apply this approach to quantify adaptive evolution of coding and noncoding sequence in Drosophila, of cis-regulatory elements in yeast, and of the seasonal influenza virus.

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