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Notes -
Yep, two individuals who have the same genome but are different at 10 phenotypically important loci will present much more differently to each other than two individuals who have the same genome but are different at 10,000 neutral loci.
Counting all loci as being equally contributing to differences in phenotype between separated groups misses the fact that the common differences between two groups have been selected to disproportionately have phenotypic impacts.
Hence you can't compare a mutation on a locus that's different between populations X and Y vs a mutation that some people in Y have and others don't and they say the impact the mutation has on the individual must be similar in both cases, hence that mutation makes people just as phenotypically different as the one which segregates the two populations.
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