## 2 Materials and Methods
### Fluorescence Measurements and Instrument Description  
Active chlorophyll fluorescence measurements were performed using a commercially available Light Induced Fluorescence Transient instrument (LIFT) (Soliense Inc, Shoreham, NY, USA; [[http://www.soliense.com/LIFT_Terrestrial.php](http://www.soliense.com/LIFT_Terrestrial.php)]([http://www.soliense.com/LIFT_Terrestrial.php](http://www.soliense.com/LIFT_Terrestrial.php))). The LIFT instrument delivers high intensity blue LED light (470 nm) to the leaf surface at a distance of up to 5 m in sequences of rapid flashlets. In a typical LIFT excitation protocol, up to 300 flashlets are delivered at high duty cycle (SQ\({}_{\mathrm{A}}\) phase), resulting in a gradual saturation of the observed fluorescence yield, roughly proportional to the increasing level of Q\({}_{\mathrm{A}}\) reduction. The next 90-120 flashlets are delivered at exponentially decreasing duty cycle (RQ\({}_{\mathrm{A}}\) phase), where the fluorescence yield relaxes, with kinetics defined by the rates of photosynthetic electron transport [22]. The entire fluorescence transient is then fitted using the fast repetition rate (FRR) model to determine maximum (Fm in dark or F'm in the light) and minimum fluorescence (Fo in dark or F' in the light) [23]. To ensure comparability with PAM, a cross-comparison of LIFT and PAM (miniPAM; Walz, Effeltrich, Germany) measurements was performed on avocado leaves (\(n=6\)) during light response curves. White light at the surface of avocado leaves was modulated from 0 to 1000 umol photons\(\cdot\)m\({}^{-2}\cdot\)s\({}^{-1}\) in 50 umol increments, with LIFT and PAM measurements performed in replicate (\(n=3\)) on adjacent leaf sections for each light intensity. To prevent cross interference from the PAM and LIFT flashes, measurements were offset by ~30 s and all but the adjacent measurement spots (~5 cm apart) masked by non-transmissible black cardboard. Cross-comparison of both LIFT and PAM showed YPSII measurements to be linearly related (R\({}^{2}\) = 0.90) and highly comparable (see supplementary material; Figure S1). For measurements of reflected leaf radiance, a QE Pro spectroradiometer (spectral range of 440 to 870 nm and spectral resolution of 0.7 nm; Ocean Optics, Dunedin, FL, USA) was mounted to the side of the LIFT instrument and optically connected via a 1 m long 400 um optical fibre. A beam splitter was installed at the optical axis of the LIFT instrument optical path to divert 20% of the incoming radiance to the QE Pro spectroradiometer, with the remainder directed to the LIFT detector. This set-up ensured that both instruments observed leaves with the same field of view (FOV). Radiometric calibration of the QE Pro spectroradiometer was performed through the optical path of the LIFT instrument at the Commonwealth Scientific Industry Research Organisation's High Resolution Plant Phenomics Centre [24].  
The LIFT instrument was operated with a non-invasive flash cycle (termed Q\({}_{\mathrm{A}}\) flash) [22] with an SQ\({}_{\mathrm{A}}\) phase consisting of 300 flashlets separated by a 1.6 \(\upmu\)s delay (~3 ms) and an RQ\({}_{\mathrm{A}}\) phase consisting of 90 flashlets with an exponential increase in the 1.6 \(\upmu\)s delay described by an exponential term of 0.5 (~300 ms). To obtain dark adapted reference Fm values, for the calculation of YNPQ and YNO, a modified flash cycle (termed PQ flash) with an SQ\({}_{\mathrm{A}}\) phase consisting of 6000 flashlets with a 20 \(\upmu\)s delay and an RQ\({}_{\mathrm{A}}\) phase identical to the Q\({}_{\mathrm{A}}\) flash (~700 ms) was used [22]; see supplementary material, Figure S1 for comparison of the Q\({}_{\mathrm{A}}\) and PQ flash to PAM. To facilitate automatic targeting and monitoring of measured leaves, the LIFT and QE Pro were mounted on a computer controlled motorized tripod (Celestron advanced VX; Celestron, Rouse Hill, NSW, Australia) and operated through custom designed software.