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What are the evolution operators, meaning allowed actions on the DNA sequence that encodes a protein.

I assume all evolution of genes is a result of duplication errors. So an answer could look somewhat like this: duplication of gene into two identical ones, omitting of nucleotide, addition of nucleotide and so on.

And some followup questions:

  1. Does this mean that originally there were very few genes and they were very short?
  2. If so - how few? How short?
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It is incorrect to assume that all evolution of proteins is a result of duplication errors. Sequences can be changed in situ as well. –  MattDMo Jun 9 '13 at 15:22
    
Also, evolution does not really act on proteins but on genes. –  terdon Jun 9 '13 at 15:36
    
@terdon and all other base sequences that have any biological function like regulatory elements. I'm not sure how this question could be answered as it seems to be based on some false premises. –  Mad Scientist Jun 9 '13 at 16:28
    
@MadScientist yes, I mean that evolution acts at the nucleotide rather than the amino acid level but felt it would be better understood by the OP if I said "genes". –  terdon Jun 9 '13 at 16:32
    
The question is simply what kind of errors does the DNA replication machine do (or other mechanism with which evolution occurs). I called it protein sequences, but of course I mean the DNA that encodes a certain protein. I rephrased for clarity. –  Uri Jun 9 '13 at 18:35
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3 Answers

up vote 1 down vote accepted

An old microbial geneticists' adage is: anything that can happen will happen, and you just need to find a way to select for what you are seeking.

A look at the Wikipedia page on mutation might be instructive.

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Looks like this is what I've been looking for. –  Uri Jun 10 '13 at 20:26
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The most frequent mechanisms are

  • Intragenic mutations: when existing genes mutate modifying gene function.
  • Gene duplication: leads to related genes in a single cell. A gene duplicates and then as two copies are available, one is free to change
  • Segment shuffling: leads to hybridisation of different DNA segments.
  • Horizontal transfer is transfer of DNA from one cell to another
  • Transduction: infection of cells by viruses or other intracellular pathogens where their DNA can integrate into the genome

You are incorrect to say all evolution occurs due to duplication. Your follow up questions are too vague. Genes can become larger or smaller, but yes as they increase so does their diversity.

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Can you please clarify the following: What exactly are intragenic mutations? What exactly is their mechanism? What is the mechanism for complete gene duplication and segment shuffling? Why didn't you mention single nucleotide errors by the replication process? –  Uri Jun 10 '13 at 20:23
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I'm assuming your question is about how proteins have evolved from their earliest forms into those that are found today. As has been stated in the comments, changes in protein primary structure occur as a consequence of changes in the nucleotide sequences of the genes that encode them. Such changes may be caused by mutation or recombination.

Mutations are changes in the nucleotide sequence that can be spontaneous, caused by errors in replication or DNA repair, or induced by mutagens such as radiation or chemicals. Recombination (non-meiotic) is the breaking and joining of different DNA strand, producing new strands with new combinations of alleles. Both these processes could result in changes in the amino acid sequence of proteins, affecting its tertiary structure and thus function. Through these processes, evolution has selected for nucleotide sequences carrying mutations that have caused beneficial changes in protein structure.

As for your follow-ups, I don't think there is an absolute answer. What is certain is that genetic complexity has increased through time, so the earliest genes that were part of a system in which a genetic code could be translated into protein are likely to have been both fewer and shorter.

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