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In speciation events, a lot of changes seems to appear simultaneously. How can a specific partial changes, occuring together with a lot of other changes, be said to be advantageous or disadvantageous?

For example, can we conclude that the loss of photolyase in placental mammals was disadvantageous? Was selection at work for that specific loss?

Another example is the change from GULO to GULOP. In an answer on Stack Exchange Biology a lot of people vote that this change was advantageous because it hadn't been selected against in natural selection, according to the book they cite.

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    $\begingroup$ Thanks for your efforts to improve the question, it looks like you've cleaned out a lot of the issues raised in the comments. I've reopened your question, though people might still suggest some improvements. It might be helpful for you to cite specific cases (including links/DOIs/etc) where scientists argue a given past change was due to selection; you mention a couple but there is no direct path from your description to where you found the information. $\endgroup$
    – Bryan Krause ♦
    Sep 9, 2019 at 21:43

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Some genetic changes occur too fast for selection to take place.

Can you please define "genetic change"? Selection can only change the frequency of alleles in a population. It cannot make a new mutation. If by, "genetic change", you mean "mutation", then selection just can't do it. If by "genetic change", you mean change in allele frequency, then the change resulting selection is not necessarily much fast than if genetic drift alone is at play.

Often scientists presume that selection has taken place for an observed genetic change. Is this assumption still valid, based on the current knowledge of genetic changes?

No, really not! Whatever you mean by "genetic change", there is no false assumption made here.

For example genetic changes caused by viruses and transposons seems to have the capacity to establish fast in populations.

Again, do you mean "mutation" or "change in allele frequency" by "genetic change"? Assuming you meant "change in allele frequency", can you please cite a peer-reviewed paper as an example but the claim is really not that obvious to me.

Can a genetic change established in a population be disadvantageous?

Yes! Most mutations are deleterious and genetic drift can lead to some drift load. No one has ever assumed that genetic drift could not happen. Even Darwin knew about it!

Can it be advantageous to make a pseudo gene functional again?

Sure! I have no idea how that relate to the rest of the question that being said.

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  • $\begingroup$ I don't know what you mean by "changing order". You are maybe confounding "mutation" with "substitution". A mutation any any sudden change to a DNA sequence. It can be a substitution, an indel, a whole chromosome duplication, whatever. You should have a look at What is the definition of a mutation? $\endgroup$
    – Remi.b
    Jul 26, 2019 at 17:22
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    $\begingroup$ Your post and comment are completely full of wrong definitions. You should probably have a look at an intro course to genetics or to evolutionary biology otherwise it is near impossible to understand what you mean. You should at least make sure you have a good understanding of the definitions of the terms: allele, gene, locus, substitution, indel, mutation, selection, and genetic drift. $\endgroup$
    – Remi.b
    Jul 26, 2019 at 17:23

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