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In their article (Context-dependent optimal substitution matrices for exposed residues (Koshi-Goldstein, 1995)), more precisely in the substitution matrix displayed in Figure 2, one one hand, the legend says: "Graphical representation of the probability of a mutation from the amino acid in a given row to that in a given column during an evolutionary time of 40 point-accepted mutations per 100 residues"

And on the other hand, I've noticed it is a lot more likely for an amino acid to be deleted than to be inserted (cf. screenshot, blue is low probability, orange/red is high probability).

enter image description here

Taken from: context-dependent optimal substitution matrices for exposed residues (Koshi-Goldstein, 1995)

How could one explain that? If that was true, all proteins sequence would slowly become smaller and smaller, right? Is it because it doesn't consider when proteins sequences merge? (I'm no biology expert, I'm sorry if the vocabulary I'm using is not exact. You are encouraged to correct me).

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  • $\begingroup$ You should always provide a complete citation; "Koshi and Goldstein" can be one of a number of papers, and you shouldn't leave it to your reader to guess, nor should you reproduce figures without a proper reference to where it came from. $\endgroup$
    – Bryan Krause
    Sep 16, 2022 at 22:03
  • $\begingroup$ I have made the necessary adjustments in my question. Thank you for your insightful feedback. $\endgroup$ Sep 16, 2022 at 22:21
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    $\begingroup$ Year is helpful but still not a complete citation. You'll want the title, journal, page numbers; these days a DOI is a nice add. And "Koshi-Goldstein" makes it appear like you are talking about one person with a hyphenated surname, not two. $\endgroup$
    – Bryan Krause
    Sep 16, 2022 at 22:35

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It seems that there IS a deletional bias across genomes Kuo & Ochman 2009:

Based on over 5,000 indel events in noncoding regions, we found that deletional events outnumbered insertions in all groups examined.

That would be one mechanism of genome shortening. However, there are mechanisms that also increase the size of the genome:

  • DNA polymerase tends to do "replication slippage". That's when DNA polymerase detaches from the DNA during replication and re-associates upstream. That way, whole genes can get duplicated (which is also a driver of evolution, since there‘s a second copy to mess around with)
  • Transposable elements (ancient viral sequences) keep replicating and re-inserting into the DNA.
  • Overall, natural selection keeps genes at full length and functional

So although small edits tend to be on the deleterious side, big edits are the opposite, causing an overall expansion of the genome.

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    $\begingroup$ Worth considering selection, too. Populations need not follow mutational biases if selection favors something different. $\endgroup$
    – Bryan Krause
    Sep 17, 2022 at 1:07

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