Appendix S1 Supplementary Methods
Trait Measurement
For each individual replicate, a shoot growing in representative light conditions of the species was
collected in the field and brought back to the lab in Ziploc bags. If a particular species in a particular
stage tended to occur in the understory, shade leaves were collected. Specific leaf area (cm2 g-1) was
calculated as the fresh leaf area to dry mass ratio, with leaf areas calculated by analyzing photos using
ImageJ software and dry weights measured after drying samples for minimum 72 hours in drying ovens.
After leaves were weighed for SLA, samples were ground to a fine powder in a wig-L bug, 4 mg
subsample weighed and encapsulated in tin, and combusted for analysis in a continuous flow IRMS (PDZ
Europa) for analysis of leaf N content (%N). The nitrogen analysis was conducted at the Center for
Stable Isotope Biogeochemistry at UC Berkeley. Wood density was measured on terminal first-year
shoots. After bark and pith were removed fresh volume was measured using by water displacement, and
sample mass determined after 3 days in the drying oven. Values used are oven-dried mass per fresh unit
volume (g cm-3).
Species means
Species means were calculated for each stage for each trait. A minimum of 3 individuals were used as
replicates for each species in each stage. The majority of species occurred in more than one stage, so
separate means were calculated for each stage to incorporate intra-specific variation as it relates to
successional status. One of our measures of functional diversity requires fewer trait dimensions than
species (functional richness, Villeger et al. 2008), thus we were limited to three functional traits by the
low species richness in early secondary plots. We used Pearson’s correlations to validate that there was
low correlation among the three focus traits, across the four stages (Table S1).
Abundance:
Abundance was measured for each species in each quadrat, by summing the basal area of all living
individuals. Relative abundance, used in calculations of functional evenness, was calculated by dividing
each species’ abundance value by sum total of basal area of the quadrat. For null models the relative
abundance structure of each quadrat was maintained, but trait associations with those abundances were
randomized. A frequency-based measure of abundance was also calculated, to estimate for each species
its distribution across the four stages. The number of individuals of a species occurring in each stage was
divided by the total number of individuals, to determine the proportion of how often that species occurred
in a particular stage. This frequency based abundance was used in the weighted draws in the null model.
Trait matrix
Our species pool included 63 species from across the 4 stages for which we had functional trait data. We
created a trait matrix such that for each species its mean trait value for each stage was a separate cell; for
stages where a species was absent the mean value across stages where it was present was entered. For
functional diversity indices these trait values were paired with the relative abundance structure of each
quadrat. The values of the three functional traits associated with a given species in a stage were assigned
together to maintain the correlation structure observed (Stubbs & Wilson 2004).
Statistical analysis
Each replicate plot was subdivided into 5 quadrats, so we incorporated a nested design in our statistical
analyses. Three of the quadrats in the youngest secondary forest site had only one or two species, so these
were excluded from the analyses. The remaining quadrats all had a minimum of four species.