# Parallel Seasonal Patterns of Photosynthesis, Fluorescence, and Reflectance Indices in Boreal Trees
## 4 Discussion
### Seasonal Kinetics
The slight NDVI variation in evergreen species across seasons was expected, as evergreen canopy structure is relatively stable over seasons [17]. The small increase in the NDVI during the emergence of new foliage in _P. bunksiana_ indicated some sensitivity to the structural changes in evergreens associated with the flush of new leaves. However, the NDVI fails to capture subtler changes in physiology (e.g., photosynthetic downregulation) [19]. The PRI was capable of tracking photosynthetic phenology for all evergreen species, and showed strong seasonal variation. These patterns were similar to seasonal trends shown in other studies that demonstrated that the PRI responds to seasonally changing chlorophyll and carotenoid pigment pool sizes [13; 14; 19]. The PRI is sensitive to changes in the chlorophyll/carotenoid ratios that are driven by the increase in carotenoids and the decline of chlorophyll concentrations in the winter, and their reversal in the summer [13]. These pigment changes are related to the cold-hardening process in response to changing temperature and photoperiod, and subsequent readjustment during the de-hardening period in the spring [6; 7; 9]. In deciduous species, the PRI variation during the spring activation was likely a result of budburst and the increase in foliage and subsequent changes in pigment levels. The initial fall decrease in the PRI to values lower than the normal winter background may have been attributed to the breakdown of chlorophyll during senescence [43]; the more rapid breakdown of chlorophylls than carotenoids during senescence [44] alters chlorophyll/carotenoid ratios, to which the PRI is sensitive. The lower values of the PRI seen in _L. laricina_ during winter periods compared to the broad-leaf deciduous species was likely due to the persistence of leaf litter on the top of the pots following senescence, causing lower values than was seen with bare soil. The CCI showed strong seasonal variation in both evergreen and deciduous species, indicating that the CCI can effectively track photosynthetic phenology in both functional types, unlike the PRI and NDVI. The close parallels between the CCI and photosynthetic activity in evergreens were consistent with other findings indicating that changes in the CCI coincide with large pigment pool size shifts [15], which are known to closely track photosynthetic rates and GPP in evergreens [13; 14; 15]. Seasonal changes in the CCI for deciduous species were primarily driven by the presence and absence of canopy foliage. Similar to the PRI, the persistence of leaf litter on the top of pots was the likely cause of lower CCI values seen in _L. laricina_, compared to broad-leaf deciduous species, during winter periods. As with other reflectance indices, the CCI was also clearly affected by snow, which could have confounded the seasonal interpretation of this index. Consequently, more work may be needed to correct for these background effects. The parallel seasonal patterns of the CCI and photosynthetic activity in deciduous species suggested that the CCI is sensitive to canopy structural changes, as well as the adjustment of pigments associated with leaf development in the spring, and senescence during the fall transition. The spikes in the CCI at the end of the spring transition for spruce species (_P. mariana_ and _P. glauca_) and later in the summer for _P. banksiana_ that coincided with needle expansion and shoot elongation indicated that the CCI is also sensitive to canopy structure in evergreens, which has not previously been reported. These results indicate that the CCI may be sensitive to a combination of canopy structural changes and pigment pool size adjustments for both functional types when tracking photosynthetic phenology. Consequently, the CCI appears well-suited to assess photosynthetic phenology consistently across evergreen, deciduous, and mixed forests, where the NDVI and PRI are likely to show different responses.