DOI: 10.5061/dryad.qz612jmpz
title: Data from: Dietary resilience of coral reef fishes to habitat degradation

description: The ability of consumers to adjust their diet in response to resource
 shifts is a key mechanism allowing the persistence of populations and the
 underlying species’ adaptive capacity. Yet on coral reefs, one of the
 marine habitats most vulnerable to global change, the extent to which
 species alter their diet remains poorly understood. Here, we integrated
 DNA-based gut content analyses (metabarcoding), otolith analysis, body
 condition, and field surveys to test how dietary versatility can mediate
 effects of habitat degradation on two invertivorous fishes: Chaetodon
 capistratus, a browser, and Hypoplectrus puella, an active predator.
 Metabarcoding revealed significant dietary variation in both species
 across reefs with different levels of coral cover. However, the response
 was more pronounced in the browser, whose diet was anthozoan-dominated on
 healthy reefs, whereas annelid-dominated on degraded reefs. We found
 slower growth and reduced body condition on degraded reefs in the browser
 but not the active predator. Our results suggest that while dietary
 versatility serves as a mechanism to cope with degraded environments, the
 degree to which dietary shifts can buffer from the effects of habitat
 degradation varies between species. Finally, we detected intraspecific
 dietary variation across sites that suggests food webs and energy flow
 differ at relatively small scales between healthy and degraded reefs.
description: # Dietary resilience of coral reef fishes to habitat degradation DOI:
 [https://doi.org/10.5061/dryad.qz612jmpz](https://doi.org/10.5061/dryad.qz612jmpz) This deposit contains sequence-based diet data, otolith (age/growth) measurements, benthic cover data collected from nine reefs in Bocas del Toro, Panama, fish length-weight and body condition (Kn) used in the study “Dietary resilience of coral reef fishes to habitat degradation.” Files included in this deposit * `curated_BCS19_phyloseq.rds` — RDS file containing a phyloseq object assembled from Illumina COI sequences of fish stomach and gut contents for two study species: *Chaetodon capistratus* and *Hypoplectrus puella*. * `bocas_diet_otoliths_all.csv` — CSV file with fish and otolith measurements used for growth/age analyses. * `bocas_benthic_quadrat_data.csv` — CSV file of benthic cover scores from photographic quadrats scored with CoralNet. * `Categories.txt` — Delimited text file mapping taxon acronyms to full taxon names and to broad benthic categories. * `bocas_fish_condition.csv` — CSV file with fish metrics and body condition (relative condition factor, Kn). Required software * The file `curated_BCS19_phyloseq.rds` contains an R phyloseq object and requires the R package phyloseq to be installed to read and use this object. * Please refer to the provided code for installing and loading the phyloseq R package and for reading the phyloseq object. Contents and variable definitions 1. bocas_benthic_quadrat_data.csv * Description: Point-based benthic cover scores derived from photographic quadrats (quadrats = 100 × 70 cm). Quadrats were placed every 2 m along 20 m transects (10 quadrats per transect), with three transects per site (reef). Each quadrat was scored at 100 points on CoralNet. * Variables (column names): * **`Site`**: Site code for one of nine reefs — ALR = Almirante; CCR = Cayo Corales; PBL = Punta Puebla; PPR = Popa Reef; PST = Stri Point; RNW = Runway; ROL = Roldan; SCR = Salt Creek; SIS = Hermanas. * **`Transect`**: Transect identifier within the site. * **`Quadrat`**: Quadrat identifier within a transect (1–10). * **`Categ`**: Benthic category assigned at the scored point. Possible values (13 categories): Dead hard coral; Grazable substrate; Live hard coral; Live soft coral; Macroalga; Other invertebrate; Rubble; Sand; Seagrass; Shade; Sponge; Unknown; Zoanthid. * **`V1`**: Abundance — number of CoralNet-scored points assigned to the `Categ` value for that record. When aggregated at the quadrat level, values range 0–100 per quadrat. 1. bocas_diet_otoliths_all.csv * Description: Fish and otolith measurement data used for otolith-based age and growth estimation for two study species: *Chaetodon capistratus* and *Hypoplectrus puella*. * Variables (column names): * **`Otolith extraction No`**: Otolith extraction ID. * **`Reef`**: Site codes for 9 study reefs: ALR = Almirante; CCR = Cayo Corales; PBL = Punta Puebla; PPR = Popa Reef; PST = Stri Point; RNW = Runway; ROL = Roldan; SCR = Salt Creek; SIS = Hermanas. * **`Zone`**: Habitat zone. Values: outer bay; inner bay; inner bay disturbed. * **`Species`**: Study species names. Values: *Chaetodon capistratus*; *Hypoplectrus puella*. * **`Fish.ID`**: Fish sample unique identifier. * **`TL_mm`**: Fish total length in millimeters (mm). * **`Total_length_otolith`**: Total length of the otolith in millimeters (mm). * **`Rings`**: Number of otolith growth rings (counted annuli). * **`Rings_average`**: Average number of growth rings (counted annuli). * **`Notes`**: Text notes. 1. Categories.txt * Description: Mapping of taxon acronyms used in benthic scoring to full taxon names and to the broad `Categ` groups used in `bocas_benthic_quadrat_data.csv`. * Variables (column names): * **`Acronym`**: Acronym used in the benthic dataset. * **`Taxon`**: Full taxon name. * **`Category`**: Benthic category (one of the 13 listed under `Categ`). 1. curated_BCS19_phyloseq.rds * Description: RDS file containing a single phyloseq object assembled from COI gut-content Illumina sequence data for *Chaetodon capistratus* and *Hypoplectrus puella*. Use `readRDS()` to load into R (phyloseq required). * phyloseq components: * sample_data (sample-level metadata). Variables (column names): * **`Run`**: Sequencing run ID. * **`Library`**: Sequencing library ID. * **`Gene`**: Gene sequenced (e.g., COI). * **`Adapter.Order`**: Adapter order number. * **`Adapter`**: Adapter ID. * **`Primer.Tag.Number`**: Primer tag number. * **`MLID`**: Sequencing sample ID. * **`Country`**: Country of sample collection. * **`Ocean`**: Ocean of sample collection. * **`Locality`**: Region of sample collection. * **`Site`**: Site ID (one of the nine reef codes listed above). * **`Subsite`**: Fish sample ID. * **`Ecosystem`**: Not used (empty in this dataset). * **`Habitat`**: Not used (empty in this dataset). * **`Size`**: Not used (NA in this dataset). * **`Fraction`**: Sample fraction/type. Values: Ccapistratus fish stomach content; Hpuella fish gut content; Hpuella fish gut tissue. (categorical) * **`Sample`**: Sample type. Values: primary; control. * **`Note`**: Not used (NA in this dataset). * **`Site.Code2`**: Redundant; retained for provenance (combined Site and Subsite identifier). * **`rootnum`**: Not used (NA in this dataset). * **`Site.Code`**: Combined Site and Subsite ID. * **`Site.Code.Size.Fraction`**: Combined Site ID, Subsite ID, and Fraction type. * **`Ecosystem.Size.Fraction`**: Redundant; retained for provenance (Sample fraction/type as in `Fraction`). * **`Sample.Date`**: Not used (NA in this dataset). * otu_table — OTU count matrix (OTUs are rows; samples are columns). * tax_table — Taxonomy table (rows = OTUs; columns = taxonomic ranks). 1. bocas_fish_condition.csv * Description: Fish length and weight data used calculating relative condition factor (Kn) for two study species: *Chaetodon capistratus* and *Hypoplectrus puella*. * Variables (column names): * **`Species`**: Study species names. Values: *Chaetodon capistratus*; *Hypoplectrus puella*. * **`Fish.ID`**: Fish sample unique identifier. * **`Wet_weight`**: Fish wet weight in (gr). * **`Wet_weight_natural_log`**: Natural log values of fish wet weight in (gr). * **`TLcm`**: Fish total length in centimeters (cm). * **`Total_length`**: Fish total length in millimeters (mm). * **`TLcm_natural_log`**: Natural log values of fish total length in centimeters (cm). * **`a`**: regression coefficient a (based on weight-length regression). * **`b`**: regression coefficient b (based on weight-length regression). * **`Predicted weight`**: Values of predicted weight used to calculate the relative nutritional condition (Kn). * **`Kn`**: Relative condition factor (Kn) values for each fish individual. * **`Reef`**: Site codes for 9 study reefs: ALR = Almirante; CCR = Cayo Corales; PBL = Punta Puebla; PPR = Popa Reef; PST = Stri Point; RNW = Runway; ROL = Roldan; SCR = Salt Creek; SIS = Hermanas. * **`Zone`**: Habitat zone. Values: outer bay; inner bay; inner bay disturbed. Code and reproducibility * R scripts used to assemble the phyloseq object, clean the data, and conduct statistical analyses are available at [https://github.com/cfrederica/bocas_diet](https://github.com/cfrederica/bocas_diet)