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Surveys were conducted using snorkel on the reef crest and the reef table, in shallow sites at depths between 1.5 and 3 meters.
\nFish community characterization
\nAll fish were identified to the species level and counted along 50 m transects, in the same habitat and area as the quadrats, parallel to the reef crest and in 1.5-5 m in depth. The transect count area extended from the sea floor to the surface of the water column and consisted of at least two 50 m long swaths surveyed sequentially at each site. For all transects in all years, the same diver Hirst counted mobile fish on a 5 m wide swath, before returning along the same transect and counting cryptic benthic fishes on a 1 m wide swath. The total lengths of all fishes were estimated to the nearest cm. For analysis of fish community structure, fish species were classified\u00a0into one of Hive trophic guilds: 1. herbivores, 2. planktivores, 3. corallivores, 4. carnivores, and 5. piscivores. Species that have a wider trophic range (omnivores) were categorized by their main food preference according to the 5 categories mentioned above. Biomass was estimated using the published length/weight relationships most appropriate for the region (Adam et al., 2011; Froese & Pauly, 2000; Kulbicki et al., 2005). Sharks and large rays were occasionally seen on transects, but their overall low abundance makes band transects a poor approach to estimate their actual numbers and contribution to biomass. Therefore elasmobranchs were recorded, but not included in our calculations here.
Fish count data for 2012, 2013 and 2014.
\nData associated with publication:\u00a0Crane\u00a0NL, Nelson\u00a0P, Abelson\u00a0A, Precoda\u00a0K, Rulmal\u00a0J\u00a0Jr, et al. (2017)\u00a0PLOS\u00a0ONE.
We compared sites using agglomerative hierarchical clustering (Ward\u2019s minimum variance method; hclust in The R Stats Package, R Core Team, 2016) based on the Bray-Curtis dissimilarity index (for benthic data) and Cao dissimilarity Index (for fish data), following the recommendations of McCune and Grace (2002). We examined the effects of anthropogenic and physical environmental factors on fish community structure using permutational multivariate analysis of variance (PERMANOVA) based on distance matrices of the fish diversity at each site. To do so, we used adonis, in the package vegan (Oksanen et al. 2016), which partitions distance matrices among potential sources of variation. We Hit linear models to these distance matrices, and evaluated the pseudo-F ratios with a permutation test. The following model, stratiHied by year to control for potential inter-annual differences, fish ~ exposure + distance + population was selected by comparing the AIC score from models with all possible combinations of the following factors related to site characteristics: exposure (lagoonal or exposed), distance (distance in kilometers from the site to the village with jurisdiction), population (number of human inhabitants of the village with jurisdiction) and index (a measure of the site\u2019s orientation with respect to the prevailing northeast trade winds), from a single factor to all 5 factors. We also examined the relationship between fish community structure and benthic cover characteristics using PERMANOVA. The number of permutations for all of these tests was set at 999.
\nBCO-DMO Data Processing Notes:
\n-Data were converted from wide format to long format
\n-nd was added to all blank cells
\n-site, date, time, and transect columns were added to incorporate the information contained in the header of the file