Analyzing model outputs
We first assessed various food web properties of the 30,000 networks
(“original webs”) to check whether the generated food webs were
reasonable. Then, we identified the linked and unlinked food webs that
persisted for 1000 growing seasons (i.e., years) and passed the
abovementioned criteria (Fig. 3), and retained only persisting taxa in
these webs (“ATN-filtered webs”). We then examined food web properties
of the ATN-filtered food webs using the last 100 years of the
simulations. We calculated the mean of the CVs of biomasses of fish
stages to characterize dynamical stability of food webs and the number
of nodes and link density to characterize food web complexity. We also
compared the unlinked and the linked webs for total fish biomass, the
mean body masses of fishes weighted by relative abundance, the number of
fish stages, and the maximum trophic levels and median predator-prey
body mass (PPMR) ratios for fish stages. We computed a surrogate of
total interaction strengths by summing up all energy flows into fish
stages from their resources, CVs and skewness of the energy flows, which
were individually normalized by the total gain of the recipient fish ,
and the slopes of biomass spectra by fitting a linear model to estimate
biomass at trophic levels as a function of body mass . The presence of
weak interactions is theorized to stabilize food webs . Less negative
slopes of biomass spectra indicate less bottom-heavy food webs (Treblico
et al. 2013), which tend to be less stable than more bottom-heavy food
webs . Some measurements were log10 transformed for
interpretability. We computed 10000 bootstrap estimates of the mean
effect sizes of a stage structure (linked – unlinked) for these metrics
by taking the differences between the means of resampled values from
persisting linked and unliked food webs.
We checked the sensitivity of the model outputs to major input
parameters (Table 1). We ran 10000 simulations for each parameter
variation (16 sets in total) using the same food web topologies as the
baseline simulations. We computed 1000 bootstrap estimates of the mean
effect sizes of a stage structure (linked – unlinked) for these metrics
by taking the differences between the means of resampled values from
persisting linked and unliked food webs and compared the mean effect
sizes with those from the baseline simulations.