The frequencies of single locus genotypes (clones) in a natural popula
tion of Daphnia pulicaria in a Minnesota lake were estimated during fi
ve months when the lake was thermally stratified in 1991. Further samp
les were collected in early August 1990 and 1992. Daphnia pulicaria we
re aggregated during daytime in two layers detected with high-frequenc
y sonar. One layer was in the metalimnion and upper hypolimnion (depth
10-15 m), the other deeper in the hypolimnion (18-22 m). The layers w
ere sampled at two locations in Long Lake on eight dates in 1991. Cell
ulose acetate electrophoresis revealed four alleles at the phosphogluc
ose isomerase (PGI) locus. Three clones occurred with sufficient frequ
ency in 3077 individuals for statistical analysis. The proportion of h
omozygous slow (SS) individuals increased with time in the deep layer
at both locations, coincident with decreasing concentrations of dissol
ved oxygen, but was nearly constant in the shallower layer, where oxyg
en was near saturation. Analysis with log-linear statistics indicated
that depth, date and the depth-date interaction were most important in
explaining the variations in clone proportions during summer. Locatio
n and the date-location interaction, although significant, were less i
mportant. Data from early August 1990 and 1992 indicated that this pat
tern may be an annual phenomenon.