How evolution builds genes from scratch

No, the four species here could basically have had the same non-genic DNA in their common ancestor, and then the non-genic DNA because it is not under purifying selection mutates a lot, so can’t be detected as homologous for sufficiently distantly related species. This original amount of non-genic DNA can also have expanded a lot along the way (intergenic DNA tends to be repetitive, which is prone to duplication, for example, curious fact right?), while continuing to mutate. And in each of those four lineages different parts expanded and evolved to become genes. There’s no reason to inflate the amount of non-genic DNA in the last common ancestor to have been present as-it-is in each of those four species. It could easily have evolved along the way.

As the species become closer related, it should become increasingly likely that you can detect homologous non-genic regions in sister taxa for the ORFan protein coding genes in their sibling.

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Larry Moran has a nice pie chart:

image

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There is no problem. You are not the one who is confused.

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Correct me if I’m wrong, but those would just be considered homologs, and not “sequences (with) divergence beyond the limits of homology detection”. No?

I also do not believe that diagram depicts the process described in the article in question. But, again, not my field so I could be wrong.