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Alternative splicing can generate many gene products from single genes, by combinatorial inclusion / exclusion of introns / gene segments. What is the evolutionary advantage of having a complex processing system that allows for alternative splicing, rather than just having more genes in the genome that directly encode the numerous protein products that an alternatively spliced gene could provide?

Noah Harrison
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    Your thinking about evolution is basically flawed. You can ask why a particular development might be advantageous to an organism in particular circumstances, but evolution isn't directed, so asking why some other mechanism didn't evolve to achieve the same thing is invalid. Nature has more than one way of killing cats, and eukaryotes make use of duplicated genes. It might help you to think about how alternative splicing is used in a eukaryotic context. – David Dec 05 '20 at 18:30
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    Does this answer your question? Why do some bad traits evolve, and good ones don't? – mgkrebbs Dec 05 '20 at 19:50
  • @mgkrebbs — The question is poor, but it is not a duplicate of the one you cite. It has nothing to do with good or bad traits as far as I am concerned, so I cannot vote to close it on that account. If I have time next week I will suggest ways of thinking about the questions it actually provokes. – David Dec 09 '20 at 21:10

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A few factors to consider will be as follows:

  1. This paper shows that compared to prokaryotes, eukaryotic genomes are resilient to the increase in genomic material. They show that the energetic cost of genome maintenance is under less selection pressure in eukartoyes compared to prokaryotes. Thus, multiple genes coding for multiple splice variants may be possible in certain cases.
  2. Gene expression is a tightly regulated process and requires production of multiple repressors, activators etc. Having multiple genes for each splice variant will require transcriptional silencing of all but one / few variants (many tissue types express a specific splice variant). You can imagine that for a large number of genes for their splice variants, regulation is going to be difficult.
  3. Introns have also been hypothesized to confer a degree of resistance to deleterious mutations as there may be no change in the protein ever if the intronic regions get mutated.
  4. Research also indicates that introns are responsible for inhibiting formation of RNA - DNA hybrids during transcription.

In summary, although having multiple genes coding for multiple splice variants is possible at the genomic level, their regulation will be difficult. Moreover, introns have been proven to be beneficial for genome integrity.

Roni Saiba
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    Energy cost arguments are really unconvincing. Think about polyploidy. I think (and have written several times) that you really have to guard against self-fulfilllment arguments on molecular evolution questions. It is like this so it must be better than (what) so any argument I can think of justifies it. – David Dec 05 '20 at 12:55
  • @David I have changed my first point and included a reference for the same. – Roni Saiba Dec 05 '20 at 14:55
  • The question asks about evolution, and makes a basic mistake of thinking that there is a goal that the organism is trying to evolve to, and that it has some sort of choice as to how to get there. All one can actually say in cases like this is what the particular advantages are for an organism that "chances" on this new possibility, and whether there are any mechanistic reasons why it might evolve rapidly — perhaps more rapidly than other mechanisms. Don't fall into traps set by poorly thought out questions. – David Dec 05 '20 at 18:22