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Re: Dinofarts / Sauropod methane emissions

 Yes, but that doesn't answer the mechanism by which it crosses the
 nuclear pore, or integrates with the nuclear chromosomes.

Again, it still happens today; numts are common. Linear DNA strands are easily thin enough to fit through a nuclear pore, and "homologous recombination" (a misnomer) is almost universal.

In vertebrates, mitochondria have a modified genetic code. Therefore, mt genes that end up in the nucleus are automatically pseudogenes. But that's not the case in many other eukaryotes.

 The nuclear envelope disappears during mitosis -

Not in all eukaryotes by far. I don't know what the plesiomorphy is.

 All of the above?

Probably all of the above at different points.