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I'm reading Yang's computational molecular evolution and in the very first chapter it says the P distance is a "simplistic distance measure" between two sequences. It is the number of different sites / the total number of sites.

However, because back mutation and multiple hits cause inaccuracy it become weak over longer distances (large number of generations to most recent common ancestor, MRCA, I guess).

"The raw proportion p is usable only for highly similar sequences, with p <0.05 (5%, approximately)."

How far back in divergence time do we have to go for this p<5% to be violated? I assume it has to do with the mutation rate right? I'm trying to get a sense of scale on this for myself. Are we talking a distance of just a few generations (within species), the distance between two closely related species, or an even greater distance?

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Yes, obviously it depends on the mutation rate, which in turn depends on the locus you are dealing with and is organism-specific. – har-wradim Feb 13 '14 at 23:55

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