Effective population sizes reported in the literature typically range from a small fraction of the adult population to about half the number of breeding adults. Theoretically, however, social structuring of genetic diversity could produce effective sizes as great as or even greater than population size. A colony of the highly social black-tailed prairie dog (Cynomys ludovicianus) was studied in the field for 16 years, and data were gathered for estimation of effective population sizes from pedigrees, demography, and allozyme alleles. Social breeding groups (“coteries”) within the colony exhibited high correlations of genes among individuals, and different coteries exhibited substantial genetic differentiation. Genetic diversity thus occurred within individuals, within coteries, and among coteries, and shifted among these levels of organization over time. “Instantaneous” estimates of effective size from short-term (annual) changes in genetic correlations were calculated from pedigree information but were not useful because they produced a wide diversity of estimates, due in part to the lack of demographic and genetic equilibrium in the colony. “Asymptotic” measures of effective population size that assumed eventual genetic equilibrium yielded relatively consistent estimates of effective sizes. For 10 years of empirical results from prairie dogs, effective population sizes from pedigrees (harmonic mean = 79.4), demographic model based on breeding groups (asymptote = 88.5), and allozyme data (harmonic mean = 88.9) were similar, and all were somewhat higher than the number of adults in the population (harmonic mean = 74.1). The colony of prairie dogs, therefore, exhibited a lower rate of loss of genetic diversity than expected, due to the genetic substructure created by the presence of social breeding groups.
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