First of all, kayaks were designed and not evolved. Evolution is imagined to proceed by random changes to a design which is then approved or rejected by the environment. Kayaks are built by humans who by virtue of experience and ability to communicate with other kayak builders have some knowledge of what makes them work. As a consequence, changes to kayak design are not random but rather, directed. So human designs can change rapidly and become optimized in a much shorter time than evolved designs.
Secondly, evolution as imagined, only benefits current conditions. That is, evolutionary fitness is potentially lost if conditions change. If there was a major change in conditions, say 500 years ago, then both the 4000 year old and 1000 year old design would have to adapt, one design having to throw 3500 years of evolution on the junk pile and the other only 500 years of evolution.
Actually, this is what happened. All kayak designs were thrown on the junk pile when modern petroleum powered boats were developed. Kayaks as a species went extinct in the arctic but mutated into recreational craft and migrated into industrial cultures to the south.
In addition, little is known about kayaks older than 400 years. So whether they evolved in the sense of "improved" in the last 4000 years is strictly speculation. I would imagine that kayaks of 3000 years ago were probably as good as kayaks 1000 years ago. I would think that one hundred to two hundred years would be sufficient to refine a design about as much as was possible. After that, improvements would be minimal.
What did probably happen in the Arctic was that conditions changed periodically. Since the kayak was a hunting craft its success had to be judged by its ability to bring its builder within range of prey. If prey changed or hunting conditions changed old adaptations might have to be discarded and replaced by new designs.
And the last big change to kayak designs happened roughly 400 years ago when European whalers showed up in the arctic, bringing with them steel tools and later, milled lumber. Steel tools allowed a range of joinery in kayak frames that was previously inaccessible.
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