Winners and losers of reef flattening: An assessment of coral reef fish species and traits

#Winners and losers of reef flattening: An assessment of coral reef fish species and traits --- Datasets include density data for 109 fish species included in the analysis, environmental data used for the density analysis, and a trait table which includes the response variables of association with relief and coral cover. ## Description of the data and file structure SpecAbund.xlsx - data used for the boosted regression tree models for fish species density. Includes all density information 109 species and all environmental variables SiteEnv.xlsx - environmental data extracted from geospatial layers and matched to fish survey sites. Already merged with the species dataset in SpecAbund.xlsx but included as a smaller file traits\_combined\_2023.xlsx - trait data and response variables used for the trait analysis. Response variables extracted from boosted regression tree models and traits derived from literature and FishBase Columns in SpecAbund and SiteEnv: site: numeric site descriptor matching NOAA Reef Visual Census sites model: factor used to subset data for two separate models - not used in these analyses Year: year of RVC fish survey Month: month of RVC fish survey Latitude: latitude of RVC fish survey Longitude: longitude of RVC fish survey Depth: depth of RVC fish survey averaged for each surveyor Region: jurisdiction of RVC fish survey. FLA KEYS = Florida Keys; DRY TORT = Dry Tortugas; SEFCRI = Southeast Florida Coral Reef Initiative (Renamed to Coral Ecological Conservation Area) Coral\_cover: percentage of benthos made up of living hard coral visually estimated by RVC surveyors Reef\_complexity: maximum hard relief measured by averaging the height of the highest rigid point above the lowest point in 8 segments of the cylinder for RVC surveys SST: minimum monthly average sea surface temperature in Celcius derived from CoRTAD database from 2012-2016 NPP: net primary productivity derived from remotely sensed chlorophyll-a from the OSU VGPM model Wave\_exposure: exposure calculated using linear wave theory Habitat\_type\_classLV0: habitat classification of each site according to the FWC Unified Reef Map level 0 Habitat\_type\_classLV2: habitat classification of each site according to the FWC Uniifed Reef Map level 2 Coral\_area\_UFRTM\_20km: area classified as reef by Unified Reef Map level 0 within 20km of each site Coral\_area\_UFRTM\_200km: area classified as reef by Unified Reef Map level 0 within 200km of each site Depth\_Sbracco: remotely sensed depth of survey sites Deepwater: euclidean distance in meters over water to the 30-meter bathymetric line FSA: euclidean distance in meters over water to the nearest fish spawning aggregation site Marina\_slips\_10km: number of marina slips over 45ft within 10km of each site Marina\_slips\_25km: number of marina slips over 45ft within 25km of each site Marine\_reserve: protected status of site; whether fishing was allowed or not Population\_20km: human population living within 20km of reef sites derived from LandScan dataset Population\_50km: human population living within 50km of reef sites derived from LandScan dataset Recreational\_fishermen\_50km: number of recreational fishing licenses within 50km of reef sites derived by zip code Tourist\_fishing: statistics from Johns et al. 2001 and publicly available dataset of hotel units in Florida Artificial\_reefs\_1km: number of artificial reefs within 1 km SG\_permits\_50km: number of recreational snapper-grouper fishing permits within 50km SG\_charter\_permits\_50km: number of commercial snapper-grouper fishing permits within 50km total\_gravity\_intercept: number of people in population centers within 500km divided by the square of travel time (same as Total\_gravity and this column was not used) Total\_gravity: number of people in population centers within 500km divided by the square of travel time Keys\_Division: sub-jurisdictions of Florida Keys including Upper, Middle, Lower Keys and Marquesas; NAs for non Florida Keys sites FKNMS: Florida Keys National Marine Sanctuary sites; NAs for non Florida Keys sites DryTortugas: Dry Tortugas sites; NAs for non-Dry Tortugas sites BNP: Biscayne National Park sites; NAs for non-BNP sites CoralECA: Coral Ecological Conservation Area sites; NAs for non-ECA sites (also known as SEFCRI) Nursery\_seagrass: connectivity of reef sites to continuous seagrass patches within 10 km Nursery\_mangroves: connectivity of reef sites to mangrove stands within 12 km connectivity: number of larva from upstream modeledto a connectivity matrix; model does not extend to further north reefs and those sites were assigned NAs Comm\_engagement: metrics of commercial engagement based on landings and permits provided by NOAA Comm\_reliance: metrics of commercial engagement based on landings and permits relative to size of fishing community provided by NOAA Rec\_engagement: metrics of recreational engagement based on landings and permits provided by NOAA Rec\_reliance: metrics of recreational engagement based on landings and permits relative to size of fishing community provided by NOAA pop\_per\_area\_reef\_20km: human population divided by area of reef within 20km Commerical\_pounds\_landed: annual number of pounds of fish reported by commercial anglers Random: random number assigned to each column; not used in final model impact: fishing impact variable derived in previous project; not used in final model YEAR: Year of RVC surveys, repeat of earlier column HABITAT\_CD: habitat code used by NOAA RVC surveys to stratify sites PCT\_CORALCOVER: percent coral cover, same as Coral\_cover column REGION: jurisdiction of RVC survey sites, repeat of earlier column MAX\_HARD\_RELIEF: maximum hard relief; same as Reef\_complexity column Columns in SpecAbund (not in SiteEnv): no.divers: number of divers for RVC survey Remaining variables are individual reef fish species that were present on at least 4% of reef surveys Columns in traits\_combined\_2023: Species: full species name with space Sp: full species name with underscore Family: family Genus: genus Spec: species epithet MaxLengthTL: maximum total length in cm for South Florida/Caribbean where available Body\_size\_max: maximum total length in cm overall - contains typos and not used MaximumLengthSL: maximum standard length in cm for South Florida/Caribbean where available MaxJuvLength: maximum length of juvenile stages AspectRatio: aspect ratio of caudal fin measured as the Area^2/Height; derived from FishBase or calculated from photos AspectRatio\_Q: aspect ratio of caudal fin measured as the Area^2/Height; derived from Quimbayo et al. 2021 Log\_AR: natural log of AspectRatio column swim\_type: combination of fins used to propel fish swim\_mode: combination of fins and body movement used to propel fish body\_shape: categorical variable describing body fineness Total.length.body.depth.ratio: numerical variable describing body fineness; calculated by total length of fish divided by height at the pectoral fin presence\_defense: binary variable of whether species has chemical or physical defenses ComDepthMax: common maximum depth of species DepthMax: maximum recorded depth of species Depth\_min: minimum recorded depth Depth\_range: DepthMax minus Depth\_min Troph: trophic level of species Trophic\_level: trophic level of species - contains typos and not used Diet.x: categorical variable of feeding type; H = Herbivore, C = Carnivore, P = Piscivore, Z = Planktivore - not used Diet.y: categorical variable of feeding type; om = omnivore, im = invertivore, is = invertivore and omnivore, pk = planktivore, hd = herbivore, fc = piscivore - not used Noctural: binary variable of whether species is active at night Diel\_activity: categorical variable of whether species is active during day, night, or both shoaling: categorical variable of group size; solitary, paired, shoaling (loose aggregation), or schooling - not used Size\_group: categorical variable of group size; solitary, paired, small group, medium group, large group Position.in.water.column: common position in water column of species level\_water: common position in water column - not used Specialist: binary variable of specialization to reef; 1 = found only on coral reefs Fished: binary variable of whether species is targeted by anglers; 1 = fished Spawn: spawning mode of species; PEL = Pelagic, BAL = Balistiform, DEM = Demersal Spawning: spawning mode of species Brackish: species found in lower salinity habitats Multihabitat: species found in habitats other than coral reefs Rafter: species larvae rafting Relief: percent contribution of maximum hard relief to overall fish density derived from density models Coral: percent contribution of coral cover to overall fish density derived from density models Cryptic: binary variable of whether species are considered cryptic and to be excluded from trait models random: random variable used to determine significance in trait models Home\_range: size of home range; mob = mobile, vmob = highly mobile; sed = sedentary ## Sharing/Access information Data was derived from the following sources: * Geospatial data was extracted using the protocols described in: Zuercher, R., D. P. Kochan, R. D. Brumbaugh, K. Freeman, R. Layko, and A. R. Harborne. 2023. Identifying correlates of coral-reef fish biomass on Florida’s Coral Reef to assess potential management actions. Aquatic Conservation: Marine and Freshwater Ecosystems 33:246–263. * Fish density data extracted from NOAA RVC Surveys: https://grunt.sefsc.noaa.gov/rvc\_analysis20/ and reproduced under open data sharing licenses. * Trait data were extracted from a variety of sources, described in the paper and shared under open data licenses. Sources include FishBase (Froese and Pauly, 2000), Quimbayo, J. P., F. C. Silva, T. C. Mendes, D. S. Ferrari, S. L. Danielski, M. G. Bender, V. Parravicini, M. Kulbicki, and S. R. Floeter. 2021. Life‐history traits, geographical range, and conservation aspects of reef fishes from the Atlantic and Eastern Pacific. Ecology 102., Green, S. J., and I. M. Côté. 2014. Trait-based diet selection: Prey behaviour and morphology predict vulnerability to predation in reef fish communities. Journal of Animal Ecology 83:1451–1460., Bridge, T. C. L., O. J. Luiz, R. R. Coleman, C. N. Kane, and R. K. Kosaki. 2016. Ecological and morphological traits predict depth-generalist fishes on coral reefs. Proceedings of the Royal Society B: Biological Sciences 283:20152332.,