Answers.Body: <p>Yes this is exactly true, proteins are ideal for deep molecular dating. DNA can suffer from compositional bias. The thing you need is a reliable tree, with strong bootstrap support. You will then calibrate it with your externally established dates.</p>
  <p>Programs such as Beast allow you to do the two simultaneously. Generally, whatever approach you take you will be required or else requested to use Beast. It is however impressive.</p>
  <p>What are you dating? Ten million years is not 'deep', however 300 million is very deep indeed for animals (Metazoa), especially so for vertebrates.</p>
  <hr />
  <p>To answer your question in general terms molecular dating tends to estimate earlier divergence against the fossil record, or against the perceived view of divergence. Molecular phylogenetics argue this is because the fossil record is not sufficiently well sampled, ie the earliest fossil is missing. Palaeontology historically had a different viewpoint.</p>
  <p>The plethora of molecular dating methods has continued, an impressive Beast based approach was recently published and I'm not clear how these changes/ improve the dating estimate. My personal view is that generally each new technique improves the accuracy of molecular dating.</p>
  <hr />
  <p>Answering the second part of your question, reconstructing the ancestral sequence at a given node is formal analysis and can be performed using ML, Bayes or parsimoney. Thus it attempts to estimate the ancestral sequence and you can then compare the mutations against extant taxa. It is perhaps better to say it establishes a robust hypothesis regarding ancestral mutations.</p>
  
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Answers.Text: Thank you for the detailed answer! I am now learning what Beast can do for me.  Btw, then I am curious: is it plausible that a species didn't evolve while some of its protein sequences dramatically evolved? If it is plausible, how could we trust the correlation between divergence time and molecular age?
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Answers.Text: Answer to first question, absolutely, however modern molecular clocks take this into account (you are thinking of a global clock which very rarely occur) - you need to check but I think Beast has a global clock option. To answer your second question, you should seek compatible external evidence to assess a given clocks accuracy, for example the fossil record which was not used for the molecular date estimate.
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Body: <p>Is it possible to infer protein-coding gene evolution age by species divergence time?</p>
  <p>For example, species A diverged 300 million years (MYA) ago from its common ancestor with species C, whilst species B diverged from C 10 MYA ago.</p>
  <p>Assume they share a protein with a similar sequence, i.e. they are  assumed to be homologous. Can I say this homologous gene in species A has an older evolution age than the homologous gene in species B?</p>
  
Tags: <phylogenetics><proteins><phylogeny>
Title: Protein-coding gene evolution age and species divergence time: are they correlated?
ThreadText: # Protein-coding gene evolution age and species divergence time: are they correlated?
  
  (Asked by: username_0 on 2022-02-08)
  
  Is it possible to infer protein-coding gene evolution age by species divergence time?
  
  For example, species A diverged 300 million years (MYA) ago from its common ancestor with species C, whilst species B diverged from C 10 MYA ago.
  
  Assume they share a protein with a similar sequence, i.e. they are assumed to be homologous. Can I say this homologous gene in species A has an older evolution age than the homologous gene in species B?
  
  **Tags:** phylogenetics, proteins, phylogeny
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2022-02-08. Score: 3 | Accepted answer
  
  Yes this is exactly true, proteins are ideal for deep molecular dating. DNA can suffer from compositional bias. The thing you need is a reliable tree, with strong bootstrap support. You will then calibrate it with your externally established dates.
  
  Programs such as Beast allow you to do the two simultaneously. Generally, whatever approach you take you will be required or else requested to use Beast. It is however impressive.
  
  What are you dating? Ten million years is not 'deep', however 300 million is very deep indeed for animals (Metazoa), especially so for vertebrates.
  
  ---
  
  To answer your question in general terms molecular dating tends to estimate earlier divergence against the fossil record, or against the perceived view of divergence. Molecular phylogenetics argue this is because the fossil record is not sufficiently well sampled, ie the earliest fossil is missing. Palaeontology historically had a different viewpoint.
  
  The plethora of molecular dating methods has continued, an impressive Beast based approach was recently published and I'm not clear how these changes/ improve the dating estimate. My personal view is that generally each new technique improves the accuracy of molecular dating.
  
  ---
  
  Answering the second part of your question, reconstructing the ancestral sequence at a given node is formal analysis and can be performed using ML, Bayes or parsimoney. Thus it attempts to estimate the ancestral sequence and you can then compare the mutations against extant taxa. It is perhaps better to say it establishes a robust hypothesis regarding ancestral mutations.
  
  > **Comments:**
  > **username_0**: Thank you for the detailed answer! I am now learning what Beast can do for me.  Btw, then I am curious: is it plausible that a species didn't evolve while some of its protein sequences dramatically evolved? If it is plausible, how could we trust the correlation between divergence time and molecular age?  
  > **username_1**: Answer to first question, absolutely, however modern molecular clocks take this into account (you are thinking of a global clock which very rarely occur) - you need to check but I think Beast has a global clock option. To answer your second question, you should seek compatible external evidence to assess a given clocks accuracy, for example the fossil record which was not used for the molecular date estimate.  
  
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