## 2 Method and Material
### Evaluation of Ground Phenology Observations  
Harvard Forest is a mixed forest dominated by red maple (_Acer rubrum_) and red oak (_Quercus rubra_), both of which are cold-deciduous trees. Harvard Forest is one of few sites that report continual phenology observations for a relatively long period. Spring phenology has been observed since 1990 for 33 species (reduced to nine after 2002). Autumn phenology observations started in 1991 and were reduced to 14 species in 2002 [32]. Spring phenology is recorded as three metrics--percentage of buds on the tree that have broken open (BBRK), percentage of leaves on the tree that are at least 75% of their total size (L75), and percentage of leaves on the tree that are greater or equal to 95% of their final size (L95). Autumn phenology is recorded as the percentage of leaves remaining on the tree that have changed color (LCOLOR), and the percentage of leaves that have fallen (LFALL). For our Agro-IBIS runs, we used observations from the dominant species (_i.e._, red maple and red oak) to characterize the temperate deciduous tree plant functional type (PFT). Following literature [13],each metric was fitted for each individual tree sample (multiple tree samples are observed for each species) to a logistic function. We calculated the Day of Year (DOY) when the fitted metrics reached particular amplitude between minimum and maximum at an interval of 10% from 10%-90% (e.g., DOY when 20% of buds have broken denoted by BBRK20, DOY when 30% of leaves have changed color denoted by LCOLOR30). Then, the average DOY of five red maple individuals and four red oak individuals was used to represent the phenology of the site. We ran a series of Agro-IBIS simulations at the Harvard Forest AmeriFlux site (42.5378\({}^{\circ}\)N, 72.1715\({}^{\circ}\)W) to determine which observation-based phenological metrics best represent the leaf onset and offset, and how well the model simulates carbon exchange with those metrics. Simulations were conducted with spring onset and autumn offset prescribed as each combination of the observation-based phenological metrics (e.g., BBRK20 as the onset and LCOLOR20 as the offset). We drove the model with a high-resolution (5 min latitude/longitude grid, \(\sim\)9 km on a side) historical climate dataset created by ZedX Inc. (Bellefonte, PA, USA), which contains daily values of the six variables required by the Agro-IBIS model--maximum and minimum air temperature, precipitation, incoming shortwave radiation, relative humidity and wind speed, over the conterminous U.S. for the period 1948-2007. More detailed information about the dataset can be found in [38]. Data from the grid cell containing the Harvard Forest AmeriFlux site were used to drive Agro-IBIS. The area where phenology is observed (42.53\({}^{\circ}\)N-42.54\({}^{\circ}\)N, 72.18\({}^{\circ}\)W-72.19\({}^{\circ}\)W) is approximately 1 km away from the Harvard Forest AmeriFlux site; however, both the phenology observation and the AmeriFlux site are located within the same grid cell of the climate dataset. We therefore assume that there was no variability in phenology within the grid cell. For each simulation, a soil spin-up was conducted so that soil carbon reached near equilibrium. Then the model was run over the period 1948-2007 with phenology simulated using the embedded phenology module for 1948-1990 and prescribed for 1991-2007. We compared the LAI simulated in Agro-IBIS with the deciduous overstory LAI (_i.e._, LAI of deciduous canopy without the effect of stems, calculated as the overall LAI measured minus the lowest LAI value during the time when no leaves exist) at the Harvard Forest AmeriFlux site. LAI measurements were taken in 1998, 1999, 2005, 2006, 2007 and 2008. Data from 2005 and 2008 were not included because the measurement records are too few in 2005 (only four) and 2008 was beyond the time period of our climate dataset. We calculated the mean percentage error (MPE) between simulated and observed LAI for each simulation.