why actually? if the majority of differences between two different species are the result of mutations, then we should see it also at the genes level and not just in the non-coding regions. since we do have evidence that the majority of changes among coding genes are neutral (which means that they fit well with neutral accumulation of mutations)why should we get a different pattern?
The majority of changes to coding sequence that stick around are neutral. Lots of other mutations didnât stick around because they were deleterious and removed by natural selection. That changes the pattern, e.g. it decreases the number of transversions seen relative to transitions, since the latter are more likely to be neutral.
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true. and this also suppose to be true for non coding regions, which is what you checked. right? so again, why should we see a different pattern if coding regions and non-coding regions suppose to show the same pattern? (since in both the majority of changes are neutral among two different species). so for instance if we check out 100 bp differences among human and chimp in coding genes and non coding regions, we should see that both are the result of accumulated mutations.
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No. A hefty majority of mutations in noncoding regions are neutral and will thus not suffer the kind of distorting effect of selection that mutations in coding regions do.
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Maybe Iâm confused, but if selection is in play here then why do we see the pattern in human to human differences?
Iâm not sure what youâre asking. We see the pattern because selection plays little role in mutations in most of the genome. We see the same pattern within humans and across species because mutations have been behaving this way for millions of years.
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so you are basically saying that the majority of amino acids difference between two different species isnt realy neutral, but actually the result of natural selection?
No, Iâm not saying that
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The majority of differences in coding regions between humans and chimpanzees are synonymous mutations (ie they code for the same amino acid).
Whether you think there is any sense for a designer to make humans and chimpanzees have mostly synonymous differences is up to you to decide.
The relevant bit is here:
are you aware that even synonymous codons have functional meaning?:
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It looks like you are correct and synonymous mutations are often beneficial or deleterious as well as neutral.
So then, given synonymous mutations often still have fitness effects, this is part of the difference between coding and noncoding regions.
Noncoding region mutations are much less likely to have fitness effects compared to coding region mutations.
Remembering that deleterious mutations pretty much donât fix, and beneficial mutations have a much higher chance of fixing, and neutral mutations having a chance of fixation of 1/N for haploid and 1/2N for diploid organisms, fitness effects greatly affect what mutations do and donât fix in coding regions as compared to noncoding regions.
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