I have a hypothesis for why this happens. Sexual reproduction has a very neat property: Recombination. Two individuals that each have one harmful mutation can through recombination have offspring without either of them. This allows removal of harmful mutations from the gene pool without terminating someones entire lineage - important when every generation comes with a decade of mutations, unlike microorganisms that are more on the scale of hours or days. However mitochondrial DNA cannot recombine, so it cannot benefit from this mechanism. Therefore it makes sense to move as much DNA as possible from the mitochondria to the nucleus. The same goes for the Y-chromosome, and could explain why it has been losing genes over time at a truly astounding pace.
> In the last 190 million years, the number of genes on the Y has plummeted from more than 1,000 to roughly 50, a loss of more than 95 percent.
> In the last 190 million years, the number of genes on the Y has plummeted from more than 1,000 to roughly 50, a loss of more than 95 percent.
https://www.quantamagazine.org/the-incredible-shrinking-sex-...