Modern evolution theory is a continuously refined system of evidence and theories that incorporates and has long since transcended "classical" Darwinism. There is no such thing as a classical Darwinist anymore, any more than there is a classical atomist anymore. Just as the theory of the atom has become far more detailed and refined since the early 20th century, so has evolution theory.
Punctuated equilibrium is fully a part of current evolution theory, but as only one among many processes, not the sole or dominant process. Hence there is no contrast anymore between gradualism and p.e.: both phenomena occur side-by-side, as has been confirmed in the fossil record. The reason is now well-known. Most mutations are neutral or fatal, so it takes a long time to hit on a beneficial mutation. But due to the fast pace of population turnover (most life forms have a life span measured in days or years, and thus an entire population can be replaced twenty times over in just a century or at most a millennium) beneficial mutations spread very rapidly, far more rapidly than the time it took to randomly hit upon that mutation in the first place. Yet the geological record is measured in the hundreds of thousands of years. Hence punctuated equilibrium: ten thousand years can go by before a major mutation develops, yet that mutation will dominate a population (driving all non-mutants extinct) in a mere few centuries, a span of time too short even to be visible in the fossil record.
Yet at the same time, many mutations gain dominance more slowly, develop at different rates (shorter lifespans and larger broods entail much more rapid rates of mutation, while rapid changes in environment can accelerate the benefit of mutations), and often don't drive the previous population extinct but migrate or occupy a different ecological niche and thus develop separately (and just as slowly) alongside the parent population. Hence not all evolution has exhibited punctuated equilibrium, as the originator of the theory (Stephen J. Gould) himself acknowledged.
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