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_Jaquen_Hgar_ t1_iwzjqm1 wrote

Reply to comment by Chance_Bluebird_5788 in How do we know the last common ancestor between two animals? by CaptainHindsight92

For any given gene the mutation rate will vary depending on how tightly “conserved” (I.e. constrained by necessity) that type of gene is. For instance the genes controlling the creation of certain cytochrome molecules used in cellular respiration are so highly conserved that they haven’t changed since our last common ancestor with the pea plant. Whereas genes controlling something superficial like skin pigmentation or shape of the pinna may diverge much more freely.

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Prae_ t1_ix1bv9h wrote

That's only one of the many challenges faced by molecular clocks, although really not the biggest one. By construction you're looking at the neutral mutations, at as many loci as possible. Modern, Bayesian statistical methods can account for different clock speeds in different genes and different species, and of course sequencing is cheaper than ever.

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CaptainHindsight92 OP t1_ix5gwla wrote

So apparently mice share a more recent common ancestor to humans than pigs but the generation times between mice and pigs are so different, surely mice have evolved more simply because it may have had 1 billion generations where as a pig may have only had 100 million? How does it take that into account surely it would suggest one had a less recent ancestor but in reality it just evolved more?

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Prae_ t1_ix5my08 wrote

Indeed, generation time is one of the big things to take into account. That's why in the early days, the estimates that the genetic clocks gave was only good enough for closely related species.

But the method has come a long way. They have "relaxed clocks" now, which take into account generation time and stuff (it's all Bayesian statistics which I don't really understand). When they compare to known fossil records, it broadly agrees. But I think even now you'd expect it to be more accurate when comparing rodents together than the whole of arthropods for example.

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CaptainHindsight92 OP t1_ix8k58s wrote

Thank you for reply it was very helpful! You don't have any recommendations to read about this do you? Where would I find information on fossil information, generation time and gene evolution? Thanks again!

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Prae_ t1_ix8tv3l wrote

Most of what I said comes from scientific reviews, so not super layman friendly.

The tree of life web project is maybe something I can point to if you are interested in phylogeny.

Otherwise, all I can say is look at papers using BEAST2, which is, from what I understand, the main tool used for inferring a philogenetic tree from DNA sequences.

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