## 4 Discussion
The effect of photorespiration on the relationship between LUE and isoprene emissions under severe drought conditions can likely disturb the ability of PRI to estimate isoprene emission and can prevent the standardization of the PRI signal, even for the same species or the same ecosystem. The lack of correlation between emissions and LUE late in the season also hinders the use of PRI as a unique estimator for the entire season. Additionally, PRI measured from satellite data represents conditions at the top of canopies, but estimates of GPP using eddy covariance are integrated over the entire canopy [50], which, together with the scatter of eddy covariance measurements, could account for some of the unexplained variability in the LUE-PRI relationship. PRI, however, was more sensitive than the MEGAN model to temporal changes in isoprene emissions, because it followed changes in LUE, so PRI could be used to improve MEGAN, consistent with previous foliar level studies where PRI combined with basal emission factors was as good a predictor of isoprenoid emissions as some standard emission models and where a combination of  
Figure 9: Schematics of the processes involved in the proposed conceptual model. The yellow arrows indicate the two pathways of energy absorbed by the photosystem involved in the model, electron transport and heat dissipation. The red arrows indicate the flux of reducing power. The blue arrows indicate the flux of carbon. Changes in flux intensities in situations are symbolically represented by changes in arrow width. Upward (downward) arrows indicate increases (decreases). The double pointed arrow indicates correlation between isoprene and PRI (CCI). These schematics are illustrative only and the arrows are not fitted to scale. The scheme does not include the effect of temperature that is one of the main drivers of isoprene emissions. MEGAN and PRI provided the best predictions [24]. PRI was thus accounting for additional residual variance not explained by the factors considered in MEGAN. Furthermore, the high temporal resolution and spatially extensive nature of remotely sensed data can help the detection of some of the spatial and temporal variability in emissions that other models may miss [24]. In addition to the diurnal relationship between PRI and LUE mediated by the xanthophyll cycle and indicating excess reducing power, seasonal changes in PRI are primarily influenced by carotenoid pool sizes (relative to chlorophyll). The relationship between PRI and isoprene emissions is strongly influenced by these constitutive changes in pigments [38], so understanding how the isoprene-PRI relationship is affected by both long-term changes in pools of carotenoid pigments and short-term dynamic adjustments of LUE is important in studies with seasonal temporal scales. MODIS PRI (CCI) has been developed to assess shifts in the levels of chlorophyll and carotenoid pigments rather than the xanthophyll de-epoxidation cycle per se, particularly when sampled over seasonal cycles in coniferous forests [37]. Knowledge of the long-term pigment changes would add information for their effect on isoprene emission, facilitating the interpretation of PRI for monitoring isoprene emissions.