# Parallel Seasonal Patterns of Photosynthesis, Fluorescence, and Reflectance Indices in Boreal Trees
## Materials and Methods
This ratio was corrected to reflectance (\(\rho_{\lambda}\)), by means of a cross-calibration procedure using \(I_{\lambda}\) and \(R_{\lambda}\) measurements (\(R_{panel\lambda}\)) from a standard reference panel (Spectralon, LabSphere, North Sutton, NH, USA) under the same conditions, immediately prior to and following sampling (Equation (1)) [37]. \[\rho_{\lambda}=\frac{R_{target_{\lambda}}}{I_{\lambda}}\;\times\;\frac{I_{ \lambda}}{R_{panel_{\lambda}}} \tag{1}\]  
Optical indices were then calculated using the canopy reflectance (\(\rho_{\lambda}\)) from each measurement. Index values were calculated utilizing 630 and 800 nm for the NDVI (Equation (2)), 532 and 570 nm for the PRI (Equation (3)), and 532 and 630 nm for the CCI (Equation (4)). The CCI was originally calculated using reflectance in MODIS bands 1 (650 nm, a terrestrial band) and 11 (530 nm, an ocean band) [15]. For this experiment, the CCI was calculated using reflectance in the 532 and 630 nm wavebands (Equation (4)). \[\mathrm{NDVI}=\frac{\rho_{800\mathrm{nm}}-\rho_{630\mathrm{nm}}}{\rho_{800 \mathrm{nm}}+\rho_{630\mathrm{nm}}} \tag{2}\]  
\[\mathrm{PRI}=\frac{\rho_{532\mathrm{nm}}-\rho_{570\mathrm{nm}}}{\rho_{532 \mathrm{nm}}+\rho_{570\mathrm{nm}}} \tag{3}\]  
\[\mathrm{CCI}=\frac{\rho_{532\mathrm{nm}}-\rho_{630\mathrm{nm}}}{\rho_{532 \mathrm{nm}}+\rho_{630\mathrm{nm}}} \tag{4}\]  
Photosynthetic rate, expressed as net CO\({}_{2}\) assimilation, was measured using a portable gas exchange system (LI-6400; LI-COR, Lincoln, NE, USA). Leaves, or bundles of leaves in the case of conifers, were placed inside a gas exchange chamber. The chamber monitored CO\({}_{2}\) assimilation rates under 1500 umol photons m\({}^{-2}\) s\({}^{-1}\) to determine light-saturated photosynthetic rate (\(P_{\mathrm{s}}\); umol CO\({}_{2}\) m\({}^{-2}\) s\({}^{-1}\)). The reference CO\({}_{2}\) was set to 400 umol mol\({}^{-1}\) to match atmospheric concentrations. The chamber air flow was set to 400 umol s\({}^{-1}\), with temperature and humidity set to match ambient conditions. Following a 1-3 min acclimation period after the leaf-clip was set on a plant, five measurements were taken from the five plants of each species. The photosynthetic rate of each species was determined by averaging the 25 measurements from all individuals of a given species at a single sampling interval. Chlorophyll fluorescence was measured using a portable fluorometer (Mini-PAM; Walz, Effeltrich, Germany) fitted with a fibre-optic and leaf-clip holder (2030-B; Walz, Effeltrich, Germany). Leaves sampled were kept as close to their original orientation as possible to maintain ambient illumination during sampling; needles were bundled together in a flat plane prior to clamping to maximize the sampling area. The fluorometer recorded Fs under ambient illumination, without a saturating pulse of light, which was used as an indicator of SIF. Eighteen samples, with three leaves, or bundles of needles, measured from six individuals were taken and averaged together for each species. Fluorescence was not sampled during winter months, when low PPFD values due to low solar elevation and building shade resulted in poor fluorescence signals. Data collected for this experiment were compared over a year to examine the seasonal course of optical indices, fluorescence, and photosynthetic activity through seasonal transitions. Data were analyzed both as time series and through regression analyses. ANCOVA were used to test differences between the slopes of the relationships of the two functional groups.