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The Y chormosome almost doesn't crossover with the X chromosome, and so the evolution of anything it encodes must be much slower, because by the Hill–Robertson effect beneficial mutations must occur sequentially in its hereditary tree, not in parallel. (That is: in that tree for the Y chromosome, there is no merging, so you can't collect all the beneficial mutations from a massive population into a single Y chromosome, as you can with other chromosomes.)

The Wikipedia page for Y chromosome lists a number of genes (mostly related to reproductive machinery), but it's hard to tell from their descriptions whether they actually provide blueprints for these items of machinery or they simply switch on/off other processes (or otherwise regulate them, but in quite a trivial way), while the blueprints themselves are actually stored in the recombinant chromosomes. That would make sense, because then the machinery would be subject to the evolutionary benefits described in the previous paragraph. But is this actually the way it is? Or maybe science does not know this for sure, as of yet?

So is a Y chromosome just a bunch of switches + some genetic garbage that allows it to be used as an ID to trace lineage?

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