Measuring differences between populations

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When individuals mate locally, different populations tend to diverge from each other in the frequencies of their alleles. Genetic differences between populations are therefore differences in allele frequencies — and these differences in allele frequencies may have consequences in terms of phenotypic or adaptive differences. But every difference in allele frequencies is not equal. When populations encompass great genetic variation, large differences in allele frequencies still leave much overlap — the individuals in the different populations may not be very different from each other. In contrast, slight differences in allele frequencies might be very important between populations that are not variable, because individuals in these populations might vary extensively as a result.

Geneticists measure the differences between populations by comparing the difference in allele frequencies to the amount of variation within the populations. When people mate with their neighbors, they tend to become more inbred — that is, they are more likely to mate with distant relatives. This means that people will tend to have greater genetic similarity than they would have if they mated equally with people who were born across the world.

Increase in the level of inbreeding due to low gene flow is often used as a statistic, called FST, relating the increase in inbreeding in the subpopulation to that in the total population. When gene flow is high, FST is low, and vice versa. FST represents the proportion of differences between two individuals taken randomly from two subpopulations that are due to the differences in allele frequency between subpopulations alone. Other differences between the individuals are those that could be found between individuals taken randomly from the same subpopulation. FST therefore provides a comparison between the between-subpopulation and within-subpopulation components of genetic variation.

The relationship of FST and migration between populations. When the forces causing genetic divergence between subpopulations are balanced by gene flow, the reduction of heterozygosity within subpopulations is a function of the number of people who move between subpopulations each generation, expressed by FST = 1 / (1 + 4Nm).

Comparing human populations taken from different continents, FST is between 0.1 and 0.15, meaning that only between 10 and 15 percent of genetic differences between individuals are attributable to their geographic origins. This difference is relatively small compared to many other large mammal species spread among different continents, such as wolves or bears Templeton:1998. This level of similarity among human populations means that they have shared high levels of gene flow in the past. However, the meaning of these numbers depends on the relationship of gene flow and the other evolutionary forces.

Because they are opposite in direction, gene flow and genetic drift will reach an equilibrium over time. At equilibrium, FST = 1 / (1 + 4Nm), where Nm is the number of migrants moving into each subpopulation. Neglecting the forces of selection and mutation, then, an FST of 0.1 for human continental populations means an average of 2 migrants have been entering each continent per generation for a long period of time. Many more people are moving from place to place today than two, so one prediction of this relationship is that the level of genetic differences among continents will in the future decrease. In the face of this gene flow, it is likely that most of the differences in allele frequencies that persist in humans are in fact affected by selection. Indeed many of the most obvious differences, related to physical appearances in different places, appear to bear this out.