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Genetic differences (Fst) between humans and other great apes

ApostateAbe

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Interesting table from the study by Fischer et al, "Demographic History and Genetic Differentiation in Apes," 2006.

Fischer_et_al_Demographic_History_and_Genetic.png


The values in the top right half are the pairwise Fst values. Fst is a metric of genetic variation between two populations. An Fst of 0.09 means that there is 9% as much genetic variation between the two populations as there is on average within each population. This table gives an Fst value of 0.89 between chimpanzees and humans, meaning 89% as much genetic variation between chimpanzees and humans as there is on average within each species. The Fst value between Chinese and the Hasau ethnic group of Africa is 0.15. πbetween seems to be similar to Fst but more of a raw value of pairwise genetic differences without respect to variation within groups, so take the 0.13 value representing the πbetween difference between Chinese and Hasau, multiply it by 9, and you get the difference between chimpanzees and humans. That kinda puts racial differences in perspective (not that any human race is more chimp-like). It takes an Fst value of only 0.57 for two populations to be two different species (the average Fst between each of the three chimp subspecies and bonobos), and major human races are reportedly an Fst of 0.12 on average, which means you need to multiply human racial variation by only 5 to get splitting of species within humans. If we were to use the πbetween values instead of the Fst values, we would need to multiply by only 3 to get speciation.

There is a myth among anti-racists that Fst is used to define subspecies, that the minimum threshold is 0.25, that human races don't meet that threshold, and therefore races are not biological. Just a myth based on misunderstandings of both Sewall Wright and Smith, Chiszar, and Montanucci, but the two biologists most responsible for spreading the myth--Alan Templeton and Joseph Graves--have been especially prolific in publishing the myth and marketing it to both academia and the public over the last 17 years. Taxonomists have generally never used genetic analyses to define subspecies, instead preferring phenotypes, mainly the traditional seventy-five-percent rule. If over 75% of the population can be identified by a morphological trait and if over 75% of the other population lacks that trait, then you have two different subspecies (Dean Amadon, "The Seventy-Five Per Cent Rule for Subspecies," 1949). Somehow, this morphed into the 0.25 Fst threshold for subspecies in the imaginations of two authors. So, if you are confused by this shit, don't feel bad. The experts are also confused by this shit.
 
The description of Fst is confusing.

89% as much variation between humans and chimpanzees as the average variation within each species suggests the average (human,chimp) pair is more closely genetically similar than either the average (human,human) pair or the average (chimp,chimp) pair.

That can't be right... :confused:
 
There are reasons why these values may seem not quite right. One possibility is that I am misunderstanding it. That is less certain. A more certain reason why these values do not fit our expectations is that they depend merely on genetic drift, time, and admixture, very little to do with phenotypic differences. The genetic markers are scattered indiscriminately over the whole genome, but 98% of the hominid genome is merely non-coding "junk" DNA. Hominid evolution happened very fast, phenotypically, but affecting only 2% of the genome, and genetic drift happened at the same slow crawl. It is one of fallacies of placing excessive significance on the Fst=0.12 for human races.
 
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