3.1 | Community-wide trophic structure metrics
We assessed trophic structure change between the historical and
contemporary San Juan River fish community using five community-wide
metrics derived to quantify and test ecologically relevant hypotheses
related to food webs (Layman et al ., 2007; Table 2). These
metrics included: δ13C range (CR),
δ15N range (NR), centroid distance (CD), nearest
neighbor distance (NND), and standard deviation of the nearest neighbor
distance (SDNND). Ranges of δ13C and
δ15N are simple metrics that measure the diversity of
assimilated basal resources and food chain length, respectively.
Centroid distance quantifies a food web’s overall resource use diversity
and is calculated as the Euclidian distance from each species’ mean
δ13C and δ15N to the global centroid
(i.e., the mean δ13C and δ15N value
for all species). Nearest neighbor distance (NND) is a measure of the
trophic similarity among species and is the mean of the shortest
Euclidian distance between each species’ δ13C and
δ15N mean. A food web with a smaller NND suggests
trophic ecologies are similar and redundant among species while a larger
NND indicates more divergent trophic niches. We also calculated the
standard deviation of the NND (SDNND) because it is less influenced by
sample size than NND. A comparably lower SDNND suggests differences in
species’ trophic niches in a food web are more evenly distributed.
To assess differences in the five community-wide trophic structure
metrics between the two periods, we used the R package SIBER(Jackson et al ., 2011) which employs a Bayesian-based Markov
Chain Monte Carlo (MCMC) algorithm to produce posterior probability
distributions for each metric of interest using observed
δ13C and δ15N values. To produce
these distributions, we used two chains of 4,000 iterations, discarded
the first 1,000 iterations, included vague priors (a normal distribution
for the mean and an inverse Wishart distribution for sigma), and tested
for model convergence using the Gelman-Rubin ratio (R-hat) using the R
package coda (Gelman and Ruben, 1992; Jackson et al .,
2011). All R-hat were <1.01. For each metric, we then
calculated the probability the difference between historical and
contemporary period trophic metric was greater than zero by subtracting
posterior probability distributions and quantified the percent of the
resultant distribution that was greater than zero. To isolate effects of
species turnover on changes to the trophic structure of the community,
we analyzed the community with (all species sampled) and without species
turnover (only the core species present in both time periods).