DOI: 10.5061/dryad.z8w9ghxmg
title: Habitat quality effects on the abundance of a coral-dwelling fish across spatial scales

description: Microhabitat-associated fishes are expected to be negatively affected by
 coral reef degradation, given that many species are coral dwellers.
 However, the factors underlying this negative impact and the spatial
 scale(s) at which it occurs are poorly understood. We explored how habitat
 quality metrics and host preferences influence fish abundance across
 multiple spatial scales, using the functionally important cleaner fish
 Elacatinus evelynae as a study species. We surveyed fish at 10 sites in
 Curaçao that varied in coral cover and health. At the microhabitat scale,
 we found that E. evelynae group size increases on large, healthy corals
 and on some coral host species, namely Montastraea cavernosa. We also
 found that, although E. evelynae can occupy at least 10 coral host
 species, it selectively inhabits just three corals: M. cavernosa,
 Colpophyllia natans, and Diploria labrynthiformis. Scaling up to explore
 goby abundance along 30-m transects, we did not find a clear relationship
 between live coral cover and goby abundance. However, goby abundance was
 substantially higher at one location with elevated coral cover and a high
 relative abundance of E. evelynae host species. Collectively, these
 results confirm that E. evelynae abundance is impacted by reef health.
 They also indicate that the species’ long-term persistence may depend on
 both the maintenance of healthy coral hosts and the gobies’ plasticity in
 host preferences on changing reefscapes. Cryptobenthic fishes such as E.
 evelynae play a vital role in the ecosystem and understanding drivers of
 their abundance is important as reefs face increased
 degradation. 
description: # Habitat quality effects on the abundance of a coral-dwelling fish across
 spatial scales
 [https://doi.org/10.5061/dryad.z8w9ghxmg](https://doi.org/10.5061/dryad.z8w9ghxmg) Code and data files are uploaded as an R Project `Analysis.Rproj`. Open the R Markdown file where data can be read in. ## Description of the data and file structure `data_benthiccover_gobies.csv` - Data on the number of *Elacatinus evelynae* and benthic categories per transect. Columns `transect_ID` to `depth` contain transect information. The column `num_gobies` contains the number of fish observed (aggregated from the observations in `data_evelynae.csv`). Columns `inv` to `coral` contain percent benthic cover by category (sum to 100). Columns `aga` to `strig` contain the percent coral cover by taxa (sum to `coral` column). | Column | Description | | :----------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | transect\_ID | Transect ID: site.transect\_number.depth | | site | Site name: CHR - CARMABI House Reef, DBO - Daaibooi, DIR - Director's Bay, DRF - Double Reef, KAL - Playa Kalki, KOK - Kokomo Beach, LAG - Playa Lagun, MAN - Playa Manzalina, MPO - Marie Pampoen, SNB - Snake Bay | | transect | Transect number 1-3 | | depth | Transect depth: 5, 7.5, and 10 m | | num\_gobies | Total number of gobies observed on the transect | | inv | Percent cover of sessile invertebrates including soft corals, sponges, anemones, etc. | | sand | Percent cover of sand | | rock | Percent cover of rocks | | oth | Percent cover of other items found on the seafloor including pipes, trash, etc. | | rub | Percent cover of rubble | | algae | Percent cover of algae including macroalgae, turf algae, and crustose coralline algae | | coral | Percent cover of all corals | | coral\_goby | Percent cover of goby-associated corals | | aga | Percent cover of *Agaricia spp.* | | ann | Percent cover of *Orbicella annularis* | | cnat | Percent cover of *Colpophyllia natans* | | dlab | Percent cover of *Diploria labrynthiformis* | | efas | Percent cover of *Eusmilia fastigiata* | | mada | Percent cover of *Madracis auretenra* | | mani | Percent cover of *Manicina areolata* | | mcav | Percent cover of *Montastraea cavernosa* | | mean | Percent cover of *Meandrina meandrites* | | orbi | Percent cover of *Orbicella spp.* (*O. franksi* & *O. faveolata*) | | past | Percent cover of *Porites astreoides* | | sid | Percent cover of *Siderastrea siderea* | | strig | Percent cover of *Pseudodiploria strigosa* | `data_evelynae.csv` - Data on microhabitats *E. evelynae* were observed on their group size. | Column | Description | | :----------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | ID | Observation ID | | dive\_date | Dive date | | transect\_ID | Transect ID: site.transect\_number.depth | | site\_name | Site name | | site\_ID | Site ID | | transect\_depth\_m | Transect depth: 5, 7.5, and 10 m | | host\_type | Host type: coral, sponge, or rock. NA value represents a transect where no gobies were observed | | host\_group | Host group for corals: Massive, brain, or plating coral. NA value represents a coral that was not identified | | host\_ID | Host ID: Coral taxa, sponge, or rock. NA value represents a coral that was not identified | | condition | Condition (corals only): 1 (degraded), 2 (intermediate), or 3 (healthy). CARMABI House Reef and Kokomo Beach have NA values because the condition was not assessed there, and sponges and rocks have NA values because the condition was assessed only for corals | | width\_1\_cm | Coral host width 1 (cm). Sponges have no value because only height was measured; NA values represent microhabitats where width could not be measured | | width\_2\_cm | Coral host width 2 (cm) - perpendicular to width 1. Sponges have no value because only height was measured; NA values represent microhabitats where width could not be measured | | height\_cm | Microhabitat height (cm). NA values represent microhabitats where height could not be measured | | num\_gobies | Group size observed on microhabitat. NA value represents a transect where no gobies were observed | ## Code `analysis_final.Rmd` - All analyses conducted are presented here.