Data visualization and statistical analyses

All statistical analyses were performed using R studio (4.2.1), PRIMER (v.7), or GraphPad Prism (v. 8.0.2). To check sphericity of the data for repeated measures ANOVA Phyto-PAM measurements were analyzed using the Mauchly test in R. If the data did not fit assumptions (p-value from Mauchly test was < 0.05), the Geisser Greenhouse correction was used (⁵⁹). Repeated measures and two-way ANOVA were run in GraphPad Prism (v. 8.0.2). GraphPad Prism was used for time point comparisons of the physiological measurements (cell counts, F_v/F_m and NPQ) within or between the strains. PRIMER (v.7) was used for non-metric multidimensional scaling (nMDS). Square-root-transformed TPM expression of all genes in the PCC7806SL genome (⁴,889) was used in calculating the similarity matrix used in the nMDS.