Beta diversity
The NMDS of the Bray-Curtis dissimilarity matrix based on beta diversity as measured by sedDNA and microscopy both displayed a similar trajectory of community change from older to more recent samples (Fig. 1A and B). Pre-1981 sediment core samples were positioned on the left side of the ordination space, and post-1982 samples were on the right. More recent sediment core samples from 1997 to 2010 were closely clustered in the bottom right quadrant (Fig. 1A). Water samples collected for microscopic analysis prior to 1978 were positioned on the left half of the ordination space, and those collected after 1979 were positioned on the right with more recent samples from 1994 to 2010 in the bottom quadrant (Fig. 1B). The lake physiochemical conditions that correlated significantly with the sedDNA dissimilarity matrix included alkalinity, SRP, and pH (p < 0.05) with r values of 0.73, 0.71 and 0.66, respectively. The microscopy dissimilarity matrix also correlated significantly with alkalinity (p < 0.001) and SRP (p < 0.05), in addition to NH4-N (p < 0.01), NO3-N, and TP (p < 0.05), with r values of 0.78, 0.48, 0.56, 0.44 and 0.50, respectively. Mean annual trends in lake physiochemical conditions are presented in Supplementary Information, Fig. S2, and statistics for the correlations between these conditions and the dissimilarity matrices are provided in Supplementary Information, Table S3.