Temporal changes in the fish community
To determine how relative total fish abundance changed over time, MaxN
values for all individual species were combined to get a single count of
individuals per BRUV replicate over the 17-year study period. Similarly,
the total number of species observed in individual BRUV drops across
years was used to determine changes in species richness over time. These
data were then fitted to separate linear mixed models (LMM) using the R
package lme4 Version 1.1-23 (Bates et al. 2020) with Time (Year;
2002-2018) as a normalised continuous predictor variable and Site (n=5)
as a random effect.
Probability of occurrence was determined for each individual species
identified in BRUVS surveys over the 17-year study period. Generalised
linear mixed models (GLMM) assuming binomial distributions were run for
each individual species and trophic guild (planktivore, herbivore,
invertivore, piscivore) for both tropical and temperate ecoregions using
the R package lme4 with Time (year; 2002-2018) as a normalised
continuous covariate and Site (n=5) as a random effect in the model.
Statistical significance for LMM and GLMM was determined using
likelihood ratios tests (alpha=0.05). Some species were rare (i.e. only
captured on BRUVS surveys < 3 times within 2002-2018) and did
not yield enough information to fit the model and were excluded from
probability models (but included in niche models below). We then
calculated the mean (± standard error) probability of occurrence for
each trophic group for both ecoregions by fitting estimates derived from
species’ GLMM models to a linear model with time as the continuous
predictor variable using the R package stats (version 3.6.0 (RCoreTeam
2020)). As an estimate of how similar trends for individual species were
to trends of their respective region/trophic guild group, we examined
the relationship between the slope estimate of each species and the
slope estimates of the respective group using Pearson’s correlation
coefficient (stats package, version 3.6.0; (RCoreTeam 2020) values given
in SI Table 2).