I've studied that proteins found in a sample as biochemical evidences for evolution. Its variation in structure and configuration can be used to date the age when that mutation occured, effectively dating the sample. But can't DNA be directly used for the process? Proteins also require transcription and translation, increasing error. I think proteins make phylogenetic detection easier, but doesn't transcription and translation give more room for error?
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$\begingroup$ A similar question has been asked previously and I supplied an answer here. Your remarks about transcription and translation errors are irrelevant. One is using the sequences of the proteins that are correctly transcribed and translated. Those that are not will probably be degraded. They will certainly not predominate. $\endgroup$– DavidCommented May 6, 2020 at 14:48
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1$\begingroup$ I think that this question for which there are already two answers encompasses yours Comparative evolutionary study: is amino acid or nucleotide comparison more useful? $\endgroup$– DavidCommented May 6, 2020 at 14:49
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$\begingroup$ Dayhoff matrices are a way of looking at the acceleration of evolution in the protein sequences. But why wouldn't you use the genetic code for pseudo time? $\endgroup$– JamesCommented Jun 5, 2020 at 14:56
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$\begingroup$ Hi and welcome to Bio.SE! I think with a little tweaking this could be a great question, and I am not sure yet if it is a duplicate as David suggests. I have voted to close this question because it is unclear what the question is. I think without an example of the problem, it cannot be answered. What studies that use protein for time have you come across? Are they carbon dating, building a phylogenetic tree, or something else? $\endgroup$– JamesCommented Jun 5, 2020 at 14:59
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Yes, you are right. Proteins are specified by DNA sequences, so DNA sequencing is a more direct way to obtain essentially the same information. Note that mutation dating via DNA or proteins is approximate. It involves a lot of assumptions about continuous rates of mutation, but in fact mutation is a stochastic process and does not have a knowable continuous rate. The sequence of mutations can be determined with high confidence, but the rate can only be determined approximately.
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$\begingroup$ No. DNA sequencing is an inferior method for evolutionary studies in general because the DNA diverges much more rapidly than protein. There is already a question on this topic. I’ll see if I can find it. $\endgroup$– DavidCommented May 6, 2020 at 14:40
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$\begingroup$ More rapid divergence does not equate to inferiority for evolutionary studies! It would (ideally) amount to a higher "clock rate", which would (ideally) amount to higher accuracy. $\endgroup$ Commented May 6, 2020 at 15:19
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$\begingroup$ See my answer to the related question which I give a link to in my comment to the poster. $\endgroup$– DavidCommented May 6, 2020 at 17:20
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$\begingroup$ This approximate time is often called pseudo-time. $\endgroup$– JamesCommented Jun 5, 2020 at 14:53