Chrysophyte cysts preserved in recent and pre-industrial lake sediment samples from 54 Muskoka-Haliburton (Ontario) lakes were used in a paleolimnological study to determine the impact of acidic precipitation and cottage development on water quality. A total of 246 cyst morphotypes were identified. Ecological preferences of cyst morphotypes were determined using multivariate statistical analysis, cluster analysis, and species-environment correlations. Recent cyst assemblages were related to water chemistry and lake morphometric variables using Redundancy Analysis (RDA). The distribution of morphotypes was related to a gradient of acid neutralising capacity (ANC), expressed through the association of variables related to buffering (i.e. longitude, watershed area, and ionic concentration) with the first axis (λ1 = 0.29). Cyst assemblages were also defined, to a lesser extent (λ2 = 0.06), by a trophic status gradient, created through the combination of total nitrogen (TN), total phosphorus (TP), volume-weighted cottage density, and lake depth variables. The identification of lakewater pH and trophic status as important determinants of cyst assemblage structure allowed for the reconstruction of acidification and eutrophication related water chemistry changes using fossil cyst assemblages. The reconstruction of pre-industrial (pre-1850) water quality conditions with fossil cyst assemblages indicated that pH significantly decreased in 24.1% of the study lakes and increased in 16.7% of the lakes. Increases in pH in more alkaline drainage basins are attributed to alkalinity generation processes induced by acidic precipitation as has been shown in other studies. Total phosphorus (TP) concentrations significantly declined in 12.9% of the lakes and increased in 16.6% of lakes. Increases in [TP] were linked to cottage development. Decreases in trophic status may be due to landuse changes, the result of the acidification occurring in the area, or warmer and drier climates. A comparison of chrysophyte cyst and diatom water quality inferences show similar trends in pH changes. There is a good agreement between diatom and chrysophyte bioindicators with respect to [TP] changes in oligotrophic lakes (< 10 μg/L); however, diatom inferences suggest that lakes with current [TP] values greater than 10 μg/L have decreased in trophic status over time, while chrysophyte reconstructions suggest that these same lakes have become more productive systems.
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