# Parallel Seasonal Patterns of Photosynthesis, Fluorescence, and Reflectance Indices in Boreal Trees
## 1 Introduction  
Forests cover approximately 4 billion hectares of the earth's land surface [1]; the circumpolar boreal forest accounts for approximately one-quarter (1132 million hectares) of that total [2]. The boreal region, known to be a substantial store of carbon [3], is experiencing a significant change in climate. The combined effects of increasing atmospheric carbon dioxide (CO\({}_{2}\)) levels and increasing temperatures associated with climate change will impact a number of plant processes [4], and these effects are amplified at higher latitudes. These changes in climate are expected to impact growing-season length, and directly influence phenology by altering the timing of seasonal transitions that are defined by changing temperatures and photoperiod [5]. In boreal forests, tree species cycle between periods of active growth and dormancy in response to a changing temperature and day-length [5]. Different vegetation types utilize contrasting mechanisms to deal with extreme seasonal variation. For deciduous species, the onset of dormancy is easily observed by changing of leaf coloring and leaf senescence, while spring activation is marked by budburst and greening of canopies. Evergreens, however, have subtler changes in foliage during seasonal transitions. To maintain their leaves going into dormancy and to avoid winter damage, needles undergo a cold hardening [6], which involves the adjustment of leaf pigments pools, primarily carotenoids and chlorophylls, in order to dissipate excess light energy during dormancy. These adjustments are then reversed leading into the growing season [7]. In addition to these seasonal changes, plants regulate photosynthetic processes in response to changing environmental conditions on shorter timescales. Under favorable conditions, light absorbed by chlorophyll is used to drive photosynthesis through photochemistry [8]. Under stress, plants have several mechanisms to dissipate excess light energy in the form of heat, known as non-photochemical quenching (NPQ) [9]. One method of dissipation is through the xanthophyll cycle, the interconversion of three carotenoid pigments to distribute absorbed light energy between productive photochemistry and non-destructive energy dissipation [9]. A small fraction of absorbed light can also be dissipated through re-emission as chlorophyll fluorescence at a longer wavelength than what is absorbed [8]. Fluorescence is driven by the amount of absorbed photosynthetically active radiation (APAR), but is also modified by NPQ [10]. Chlorophyll fluorescence acts rapidly, dissipating energy within nanoseconds in response to changing light, and adjusting to steady-state levels over minutes [11], whereas the xanthophyll cycle acts on timescales from minutes to hours [12]. Pigment pool sizes and foliage structure adjust on longer timescales, from hours to seasons [13; 14; 15]. Together, these mechanisms of energy regulation provide several possible ways of assessing changing photosynthetic activity through optical remote sensing. The normalized difference vegetation index (NDVI) is often used to track changing vegetation \"greenness\" as a surrogate for photosynthetic activity, and has been shown to track long-term changes in growing-season length and productivity in high latitudes [16]. In deciduous vegetation, the NDVI tracks seasonal phenology of green biomass, from budburst to senescence [17]. The NDVI utilizes reflectance in red and near-infrared wavelengths to estimate the fraction of photosynthetically active radiation (f\({}_{\text{PAR}}\)) that is absorbed by green plant material [18]. Though the NDVI can detect structural changes, such as the leaf area index and f\({}_{\text{PAR}}\)[17; 18], it misses less visible changes in physiological processes controlling photosynthetic activity, particularly in evergreen species [15; 19] that see little change in greenness from spring budburst through the growing season and into winter dormancy [20].