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Most variation is neutral and due to genetic drift and the accumulation of, new, mostly neutral allele variants. This doesn't change the fact that people can vary genetically on socially relevant traits like height, IQ and skin color despite being genetically similar.
Amazonians are relatively light skinned, but nearly identical genetically to their dark skinned Peruvian neighbors. Both Europeans and North East Asians are light skinned due to convergent evolution despite their large genetic differences. Both Peruvians and Amazonians are genetically more similar to Europeans than they are to North East Asians, because they have a lot Ancestral North Eurasian ancestry from people who used to live in Siberia, the same as Europeans.
Yet they don't look or act more like Europeans than the North East Asians do, because of culture and selection and the fact most variation is neutral.
wrong e.g. here: https://en.wikipedia.org/wiki/File:Genetic_similarities_between_51_worldwide_human_populations_(Euclidean_genetic_distance_using_289,160_SNPs).png
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I'm pretty sure you're wrong on this, Amerindians are somewhat closer to East Asians than Europeans. People living in Siberia weren't same as Europeans. and Amerindians are product of mixing of Siberians and proto-East Asians.
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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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