Many species of planktonic cladocerans display substantial variation i
n habitat use (mean depth and diel vertical migration), both among and
within populations. We examined whether clonal segregation and specia
lization contributes to such behavioral variation within several lake
populations of the cladoceran, Daphnia pulicaria. Electrophoretic and
quantitative genetic analysis of clonal lines isolated from different
depths at night revealed that clonal habitat specialization was common
. Clones that utilized shallow water at night were genetically smaller
at maturity and lower fecundity under standard laboratory conditions
than the deep-water clones. The magnitude of this clonal habitat speci
alization varied among lakes: populations displaying broad use of dept
h habitats contained greater genetic variance than populations with mo
re constrained habitat use. These results are consistent with known di
fferences in selective factors in different depth habitats and suggest
that substantial clonal specialization can occur within single popula
tions. Since previous work has discovered a heritable basis to habitat
selection in several Daphnia species, including D. pulicaria in our s
tudy lakes, it is likely that clonal/depth specialization is an import
ant factor affecting the trophic ecology of Daphnia.