Segregating Sites in the Two-Subpopulation Model

Using the two subpopulation model, the expected numbers of segregating sites in a number of DNA sequences randomly sampled from a subdivided population were examined for several types of population subdivisions. It is shown that, in the case where the pattern of migration is symmetrical such as the finite island model, the expected number of segregating sites is independent of the migration rate when two or three DNA sequences are randomly sampled from the same subpopulation, but depends on the migration rate when more than three DNA sequences are sampled. It is also shown that the population subdivision can increase the amount of DNA polymorphism even in a subpopulation in some cases. T HE amount of DNA polymorphism in a population can be measured by the average number of (pairwise) nucleotide differences or the number of segregating sites in a sample. Although their statistical properties are already known, they have been obtained under the assumption of random mating population (WATTERSON 1975; TAJIMA 1983). Natural populations, however, are often subdivided into a number of subpopulations. LI (1976) has studied the distribution of nucleotide differences between two randomly chosen DNA sequences in a subdivided population by using the finite island model (MARUYAMA 1970; LATTER 1973; NEI 1975). Although his results give useful information on DNA polymorphism in a subdivided population, it is not clear whether or not they can be applied to the case where more than two DNA sequences are sampled from the population. In this paper I shall examine the expected number of segregating sites in a number of DNA sequences randomly sampled from a subdivided population by using the two subpopulation model (NEI and FELDMAN 1972; LI and NEI 1975, 1977). Although one of the main reasons, why the two subpopulation model is used instead of the other models such as the infinite island model (WRIGHT 1931), the finite island model and the stepping stone model (KIMURA and WEISS 1964; WEISS and KIMURA 1965; MARUYAMA 1969, 1977), is its simplicity, this model has the advantage of being flexible, as will be shown later.