Justin’s Notes

Population Genetics

The study of genetic variation and differences within and between human populations.

The results are quite remarkable. The mean” proportion of the total species diversity that is contained within populations is 85.4%, with a maximum of 99.7% for the Xm gene, and a minimum of 63.6% for Duffy. Less than 15% of all human genetic diversity is accounted for by differences between human groups! Moreover, the difference between populations within a race accounts for an additional 8.3%, so that only 6.3% is accounted for by racial classification. This allocation of 85% of human genetic diversity to individual variation within populations is sensitive to the sample of populations considered. As we have several times pointed out, our sample is heavily weighted with “primitive” peoples with small populations, so that their Ho values count much too heavily compared with their proportion in the total human population. Scanning Table 3 we see that, more often than not, the Hpop values are lower for South Asian aborigines, Australian aborigines, Oceanians, and Amerinds than for the three large racial groups. Moreover, the total human diversity, Hspecies, is inflated because of the overweighting of these small groups, which tend to have gene frequencies that deviate from the large races. Thus the fraction of diversity within populations is doubly underestimated since the numerator of that fraction is underestimated and the denominator overestimated. When we consider the remaining diversity, not explained by within-population effects, the allocation to within-race and between-race effects is sensitive to our racial representations. On the one hand the over-representation of aborigines and Oceanians tends to give too much weight to diversity between races. On the other hand, the racial component is underestimated by certain arbitrary lumpings of divergent populations in one race. For example, if the Hindi and Urdu speaking peoples were separated out as a race, and if the Melanesian peoples of the South Asian seas were not lumped with the Oceanians, then the racial component of diversity would be increased. Of course, by assigning each population to separate races we would carry this procedure to the reductio ad absurdum. A post facto assignment, based on gene frequencies, would also increase the racial component, but if this were carried out objectively it would lump certain Africans with Lapps! Clearly, if we are to assess the meaning of racial classifications in genetic terms, we must concern ourselves with the usual racial divisions. All things considered, then, the 6.3% of human diversity assignable to race is about right, or a slight overestimate considering that Hpop is overestimated. It is clear that our perception of relatively large differences between human races and subgroups, as compared to the variation within these groups, is indeed a biased perception and that, based on randomly chosen genetic differences, human races and populations are remarkably similar to each other, with the largest part by far of human variation being accounted for by the differences between individuals. Human racial classification is of no social value and is positively destructive of social and human relations. Since such racial classification is now seen to be of virtually no genetic or taxonomic significance either, no justification can be offered for its continuance.
— Lewontin

In brief, Lewontin ignored the fact that differences among human populations are correlated. Although population variation at any one genetic locus tends to be small, global population structure becomes clear if one examines correlated differences across loci. For a simple analogy, consider men and women’s faces. If one takes any particular characteristic, say nose size, there is likely to be more variation within a sex than between the sexes (and it would be nearly impossible to classify faces by sex with any accuracy using only nose size). However, if one considers all facial characteristics together (which is, after all, how we actually experience human faces), then sex differences become sufficiently clear that an observer can guess the correct sex more than 95 percent of the time.

— Bo Winegard, Noah Carl Superior: The Return of Race Science—A Review

A more plausible conception of race, one that is consistent with how careful philosophers and geneticists use the term, recognises that: When humans began leaving Africa around 75,000 years ago, they dispersed across a much greater range of environments than they had previously inhabited. The humans that settled in different geographic regions subsequently came under different selection pressures (e.g. temperature, seasonality, altitude). Natural barriers such as oceans (e.g. the Atlantic), deserts (e.g. the Sahara) and mountain ranges (e.g. the Himalayas) impeded gene flow between different populations for substantial periods of time. When there is limited gene flow between populations that have come under different selection pressures, we would expect them to gradually diverge from one another over via the processes of genetic drift and natural selection.

— Bo Winegard, Noah Carl Superior: The Return of Race Science—A Review
The primary reason that natural philosophers began to classify humans into different races is that human populations look different from one another. Their skin colors, hair textures, facial structures, and stature all differ, often in predictable ways. Furthermore, these differences reflect their divergent geographical origins. In fact, researchers can classify human variation by continent quite accurately using only data from the human skull. (They are able to correctly classify human skulls into black and white Americans with about 80% accuracy, using only two variables.) Therefore, despite the common charge that racial classification is ipso facto racist, and that most Enlightenment typologies of human variety were motivated by prejudices and a desire to rationalize imperial domination, ordinary people and Enlightenment philosophers also took to classifying human differences for the mundane reason that such differences actually exist.
— Bo Winegard, Noah Carl Superior: The Return of Race Science—A Review
The past 30 years of research in intelligence has produced a wealth of knowledge about the causes and consequences of differences in intelligence between individuals, and today mainstream opinion is that individual differences in intelligence are caused by both genetic and environmental influences. Much more contentious is the discussion over the cause of mean intelligence differences between racial or ethnic groups. In contrast to the general consensus that interindividual differences are both genetic and environmental in origin, some claim that mean intelligence differences between racial groups are completely environmental in origin, whereas others postulate a mix of genetic and environmental causes. In this article I discuss 5 lines of research that provide evidence that mean differences in intelligence between racial and ethnic groups are partially genetic. These lines of evidence are findings in support of Spearman’s hypothesis, consistent results from tests of measurement invariance across American racial groups, the mathematical relationship that exists for between-group and within-group sources of heritability, genomic data derived from genome-wide association studies of intelligence and polygenic scores applied to diverse samples, and admixture studies. I also discuss future potential lines of evidence regarding the causes of average group differences across racial groups. However, the data are not fully conclusive, and the exact degree to which genes influence intergroup mean differences in intelligence is not known. This discussion applies only to native English speakers born in the United States and not necessarily to any other human populations.
— Russell Warne Between-Group Mean Differences in Intelligence in the United States Are >0% Genetically Caused: Five Converging Lines of Evidence
obvious: As long as most scientists accepted the ancient division of races, they expected important genetic differences. But the recent origin of races… squares well with the minor genetic differences now measured. Human groups do vary strikingly in a few highly visible characters (skin color, hair form)—and this may fool us into thinking that overall differences must be great. But we now know that our usual metaphor of superficiality—skin deep—is literally
— Gould
It is clear that our perception of relatively large differences between human races and subgroups, as compared to the variation within these groups, is indeed a biased perception and that, based on randomly chosen genetic differences, human races and populations are remarkably similar to each other, with the largest part by far of human variation being accounted for by the differences between individuals. Human racial classification is of no social value and is positively destructive of social and human relations. Since such racial classification is now seen to be of virtually no genetic or taxonomic significance either, no justification can be offered for its
— Lewontin
Ancient DNA has transformed our understanding of population history, but its potential to reveal as much about human evolutionary biology has not been realized because of limited sample sizes and the difficulty of distinguishing sustained rises in allele frequency increasing fitness—directional selection—from shifts due to migrations, population structure, or non-adaptive purifying or stabilizing selection. Here we present a method for detecting directional selection in ancient DNA time-series data that tests for consistent trends in allele frequency change over time, and apply it to 15,836 West Eurasians (10,016 with new data). Previous work has shown that classic hard sweeps driving advantageous mutations to fixation have been rare over the broad span of human evolution8,9. By contrast, in the past ten millennia, we find that many hundreds of alleles have been affected by strong directional selection. We also document one-standard-deviation changes on the scale of modern variation in combinations of alleles that today predict complex traits. This includes decreases in predicted body fat and schizophrenia, and increases in measures of cognitive performance. These effects were measured in industrialized societies, and it remains unclear how these relate to phenotypes that were adaptive in the past. We estimate selection coefficients at 9.7 million variants, enabling study of how Darwinian forces couple to allelic effects and shape the genetic architecture of complex traits.
Ancient DNA reveals pervasive directional selection across West Eurasia
The orthodoxy maintains that the average genetic differences among people grouped according to today’s racial terms are so trivial when it comes to any meaningful biological traits that those differences can be ignored. The orthodoxy goes further, holding that we should be anxious about any research into genetic differences among populations. The concern is that such research, no matter how well-intentioned, is located on a slippery slope that leads to the kinds of pseudoscientific arguments about biological difference that were used in the past to try to justify the slave trade, the eugenics movement and the Nazis’ murder of six million Jews. I have deep sympathy for the concern that genetic discoveries could be misused to justify racism. But as a geneticist I also know that it is simply no longer possible to ignore average genetic differences among “races.”
— David Reich How Genetics Is Changing Our Understanding of 'Race'