Y-linked, X-linked, and autosomal microsatellite variation in chimpanzees (Pan troglodytes)

Microsatellites are short arrays of tandemly repeated DNA. This dissertation explores the utility of microsatellites in reconstructing the evolutionary history of the chimpanzees (Pan troglodytes). 106 male and 108 female chimpanzees were genotyped using 11 Y-linked and nine X-linked microsatellite loci that were initially isolated in humans. A subset of these individuals was genotyped using nine autosomal microsatellite loci, and these data were supplemented with previously published autosomal data (Ely et al. 1998).; Most of the human microsatellite primers amplified polymorphic homologous loci in chimpanzees. The allele sizes and genetic diversity indices for these loci were similar in chimpanzees and humans. My data suggest that discrepancies reported in previous studies, indicating smaller allele sizes and a reduction in diversity in chimpanzees relative to humans, may have arisen through sampling biases associated with using only one chimpanzee subspecies to represent the entire species. Unlike previous studies, my chimpanzee sample includes representatives from all four subspecies.; Microsatellite markers from three chromosomal elements—the Y chromosome, the X chromosome, and the autosomes—were investigated for their ability to reconstruct the phylogenetic relationships among the different subspecies. The autosomal loci proved most useful for this purpose, although there is a suggestion that the Y-linked markers may be useful for discrimination among more closely related taxa. I demonstrate the utility of choosing markers for phylogenetic reconstructions by first building trees using single-locus genotypes. While the discriminatory powers of the few loci I used were not absolute, this research indicates that microsatellites should be further investigated for this purpose, rather than dismissed because of their high degrees of homoplasy.; I also use the mutation rate ratios of the Y-linked, X-linked, and autosomal microsatellite loci to test the “male-driven model of molecular evolution” of Miyata and colleagues (1987). The three male-to-female mutation rate ratios, α, calculated using these values are dissimilar, suggesting that the male-driven model does not apply to these data. However, the Y-linked loci appear to be more variable than the autosomal and X-linked loci. A number of possibilities are explored to account for the results obtained.