Nine lakes in northern Wisconsin were sampled from February through Septemb
er 1996, and HPLC analysis of water column pigments was carried out on epil
imnetic seston, pigment distributions were evaluated throughout the water c
olumn during summer in Crystal Lake and Little Rock Lake. The purpose of ou
r study was to investigate the use of phytopigments as markers of the main
taxonomic groups of algae, As a first approach, multiple regression of mark
er pigments against chlorophyll a (chl a) was used to derive the best linea
r combination of the main xanthophylls (peridinin, fucoxanthin, alloxanthin
, lutein, and zeaxanthin), A significant regression equation (r(2) = 0.98)
was obtained for epilimnion data. The good fit indicates that the chi a:xan
thophyll ratios were fairly constant in the epilimnion of the nine lakes ov
er time. Chlorophyll a recalculated from the main xanthophylls in each samp
le showed good agreement with measured chi a in epilimnetic waters, A secon
d approach used the CHEMTAX program to analyze the same data set. CHEMTAX p
rovided estimates of chi a biomass for all algal classes and allowed distin
ction between diatoms and chrysophytes, and between chlorophytes and euglen
ophytes. These results showed a reasonably good agreement with biomass esti
mates from microscope counts, despite uncertainties associated with differe
nces in sampling procedure. Changes of pigment ratios over time in the epil
imnetic waters were also investigated, as well as differences between surfa
ce and deep samples of Little Rock Lake and Crystal Lake. We found evidence
that changes in the ratio of photoprotective pigments to chi a occurred as
a response to changes in light climate. Changes were also observed for cer
tain light-harvesting pigments. The comparison between multiple regression
and CHEMTAX analyses for inferring chl a biomass from concentrations of mar
ker pigments highlighted the need to take account of variations in pigment
ratio, as well as the need to acquire additional data on the pig ment compo
sition of planktonic algae.