# Parallel Seasonal Patterns of Photosynthesis, Fluorescence, and Reflectance Indices in Boreal Trees
## 4 Discussion
### Other Causes of Variation in Stand-Level Sampling  
While optical measurements can be used at both the leaf- and stand-levels as metrics of photosynthetic activity, there can be subtle differences in leaf- and canopy-level responses [14; 15]. In our study, one likely cause of variation was the expansion of new branches and leaf tissues, which would have affected leaf- and canopy-level signals differently.  
Presumably, background signals (including soil, leaf litter, bark, and snow) also impacted optical measurements at the canopy- and stand-levels. While the NDVI and PRI are known to be influenced by these background signals [51; 52], the effects of background signals on the CCI, while not as well-understood, were clearly visible.  
The presence of snowfall had noticeable impacts on all optical indices during winter months, which has been previously reported for the NDVI [53], but not for the PRI nor CCI. During transition periods, snowfall can obscure changes in vegetation [53], and observing patterns of spring activation and fall downregulation becomes more challenging, particularly for reflectance indices that are clearly influenced by the high albedo of snow. The impacts of different background signals on canopy-level optical indices, including snowfall in higher-latitude temperate forests, must be considered when sampling over large spatial and temporal scales.  
The measurements of leaf-level F\({}_{\rm S}\) using the PAM method had potential limitations that require further consideration [10]. Compared to other fluorescence parameters (e.g., Fm, Fv/Fm), F\({}_{\rm S}\) tells little about underlying plant physiological processes on its own [54], and it changed rapidly according to light conditions. Unlike SIF, which is measured passively using spectrometers with very narrow bandwidth, PAM fluorescence is a broadband measurement isolated with a modulated light signal. However, unlike other PAM fluorescence parameters, but similar to SIF, F\({}_{\rm S}\) is measured under ambient sunlight without the application of a saturating pulse. The passive nature of F\({}_{\rm S}\) in ambient light makes it a more appropriate analogue to SIF than other PAM fluorescence metrics that require a saturating light pulse. In this study, F\({}_{\rm S}\) was used in place of a spectral fluorescence metric due to the lack of high spectral resolution from the spectrometers utilized in this study. Future studies should investigate the seasonal responses of both F\({}\)s and SIF in response to seasonally changing conditions.  
Some aspects of this study may not be reflective of natural environmental conditions due to the small-scale and synthetic nature of the design, limiting the ability to draw direct conclusions for natural forests. Our study took place on a rooftop, where the average temperature was often warmer than that of natural forests in the same region, potentially resulting in a slightly longer growing season than would normally be seen. Presumably, other aspects of surface energy balance were also different between rooftop conditions and natural forest environments. Our plants were well-watered with periodic nutrient applications to ensure proper growth. In natural environments, plants would be exposed to a wide range of water and nutrient conditions, and would experience drought and nutrient stress, which would impact plant physiology and optical properties. Accordingly, proper extension and application of these must be done in natural ecosystems at larger scales. To investigate the potential for upscaling, further studies are underway using satellite data and the flux tower network [15].