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).