Parrotfishes were surveyed using two different methods: the Reef Visual Census program (See Smith et al 2011 and Brandt et al 2009 and https://grunt.sefsc.noaa.gov/rvc_analysis20/ for more information about this program) has been conducting a visual survey of reef fish species throughout the Florida Keys since 1978. The roving diver survey (see Adam et al 2015) was used in 2013 to collect data on parrotfishes only at several reefs in the Upper Florida Keys. Both datasets provide information on number of parrotfishes per unit area in selected locations in the Florida Keys. Parrotfish foraging parameters were also derived from behavioral observations of parrotfish feeding. See Adam et al 2015, 2018 for more details.

To better understand the functional roles of parrotfishes on Caribbean coral reefs we documented abundance, habitat preferences, and diets of nine species of parrotfishes (Scarus coelestinus, Scarus coeruleus, Scarus guacamaia, Scarus taeniopterus, Scarus vetula, Sparisoma aurofrenatum, Sparisoma chrysopterum, Sparisoma rubripinne, Sparisoma viride) on three high-relief spur-and-groove reefs (Molasses, Carysfort, and Elbow) offshore of Key Largo in the Florida Keys National Marine Sanctuary. On each reef, we conducted fish surveys, behavioral observations, and benthic surveys in three habitat types: high-relief spur and groove (depth 2 - 6 m), low-relief carbonate platform/hardbottom (depth 4 - 12 m), and carbonate boulder/rubble fields (depth 4 - 9 m). In addition, fish surveys were also conducted on a fourth high-relief spur-and-groove reef (French). We estimated parrotfish abundance in each of the three habitat types in order to assess the relative abundance and biomass of different species and to quantify differences in habitat selection. To estimate parrotfish density, we conducted 20 to 30 minute timed swims while towing a GPS receiver on a float on the surface to calculate the amount of area sampled. During a swim the observer would swim parallel with the habitat type being sampled and count and estimate the size to the nearest cm of all parrotfishes greater than or equal to 15 cm in length that were encountered in a 5 m wide swath. To quantify parrotfish behavior, approximately six individuals of each species were observed at each site for 20 min each. Foraging behavior was recorded by a SCUBA diver while towing a GPS receiver (Garmin GPS 72) attached to a surface float, which obtained position fixes of the focal fish at 15 s intervals. Fish were followed from a close distance (~ 2 m when possible), and food items were identified to the lowest taxonomic level possible, with macroalgae and coral usually identified to genus or species. Many bites involved scraping or excavating substrate colonized by a multi-species assemblage of filamentous “turf†algae and crustose coralline algae (CCA). Thus, multiple species of filamentous algae, endolithic algae, and CCA could be harvested in a single bite, and it was impossible to determine the specific species of algae targeted. We also recorded the type of substrate targeted during each foraging bout, categorizing each substrate as one of the following: (1) dead coral, (2) coral pavement, (3) boulder, (4) rubble, or (5) ledge. Dead coral included both convex and concave surfaces on the vertical and horizontal planes of three dimensional coral skeletons (primarily dead Acropora palmata) that were attached to reef substrate. Coral pavement was carbonate reef with little topographic complexity (i.e., flat limestone pavement). Boulder was large remnants of dead mounding corals not clearly attached to the bottom and often partially buried in sand. Coral rubble consisted of small dead coral fragments (generally < 10 cm in any dimension) that could be moved with minimal force. Ledges consisted entirely of the undercut sides of large spurs in the high-relief spur and groove habitat. In order to quantify the relative abundance of different food types, we estimated the percent cover of algae, coral, and other sessile invertebrates on each of the five substrates commonly targeted by parrotfishes (dead coral, coral pavement, boulder, rubble, or ledge) in 0.5 m x 0.5 m photoquadrats. We photographed a total of 8 haphazardly selected quadrats dispersed throughout the study site for each substrate type at each of the three sites (N = 24 quadrats per substrate type, N = 120 quadrats total). Each photoquadrat was divided into sixteen 12 cm x 12 cm sections which were individually photographed, and percent cover was estimated from 9 stratified random points per section (N = 144 point per quadrat).

Parrotfishes are widely considered to be important grazers on coral reefs that remove autotrophic biomass from the reef substrate and create bare space that is conducive to larval coral settlement and recruitment. Because of the top-down effects associated with their benthic foraging, this has been a major focus of parrotfish research. Another aspect of parrotfish foraging and trophic ecology that has received very little attention is coprophagy, the consumption of fecal matter. The feces of planktivorous fishes, including Chromis spp., have been identified as important sources of nutrients and trace elements to tropical and temperate reef ecosystems. Their feces are readily consumed by a variety of fishes, including parrotfishes. Although parrotfish coprophagy has been observed in prior studies, its frequency has not yet been quantified. In this study, we observed foraging in five parrotfishes on the fringing reefs of Bonaire, Netherlands: Scarus iseri, Scarus taeniopterus, Scarus vetula, Sparisoma aurofrenatum, and Sparisoma viride. For three of these species, we observed individuals of both ontogenetic phases (terminal and initial phase) to investigate ontogenetic differences in foraging. We found that coprophagy was common in four of these species (Sc. iseri, Sc. taeniopterus, Sc. vetula, and Sp. aurofrenatum), occurring in 46-90% of individuals (Sc. vetula and Sc. taeniopterus, respectively). Though we did not identify the origin of every fecal pellet consumed, we directly observed focal fishes targeting fecal pellets produced by planktivorous Chromis spp. that were often seen schooling above the reef during this feeding behavior. Additionally, most of the fecal pellets consumed by the parrotfishes were similar in appearance (i.e., relative size, shape, coloration, and consistency) to the feces produced by Chromis spp., predominantly Chromis multilineata, suggesting this common origin. However, bites on fecal matter were a relatively small proportion of the total bites taken by these species (< 5%). In contrast, a majority of bites taken by these species were taken on substrates classified as eplithic algal matrix (EAM) or crustose coralline algae (68.5-90.6% of total bites across all five species). Despite being an infrequent target of parrotfish foraging, we estimated that daily fecal C consumption is equivalent to approximately 27% of the daily algal C intake by parrotfishes targeting the major benthic foraging targets of parrotfishes (large turfs, small turfs on endolithic algae or crustose coralline algae, and crustose coralline algae) in Bonaire. The feces of plantivorous reef fishes like Chromis spp. are also likely a valuable source of nutrients to reef fishes, because the fecese of Chromis spp. has higher protein and lipid content and lower C:N and C:P than many benthic marine algae and cyanobacteria, including from the tropics. The absence of coprophagy in Sp. viride and reduced rates of coprophagy in Sc. vetula relative to the other coprophagic species could be the result of increased access to protein-rich endolithic components of the benthos. Access to endolithic components of the benthos increases with body size and the ability to excavate benthic substrate while foraging. Sparisoma viride is an important excavating parrotfish on Caribbean coral reefs, and Sc. vetula is generally larger than the other coprophagic species in our study. Future work should attempt to further quantify the contribution of fecal matter to the nutrition of parrotfishes relative to benthic foraging targets in order to provide a more complete understanding of parrotfish nutritional ecology and to elucidate the importance of coprophagy in nutrient recycling and retention on coral reefs.

Methods Data were collected across 5 fringing reef sites in Bonaire, NL: Angel City (AC; 12.10305º, -68.28852º), Aquarius (AQ; 12.09824º, -68.28624º), Bachelor’s Beach (BB; 12.12605º, -68.28819º), Invisibles (IV; 12.07805º, -68.28175º), and The Lake (TL; 12.10618º, -68.29079º) during May-July 2019.

We conducted visual censuses of initial and terminal phase parrotfish (forklength > 6 cm) along eight 100-m2 (25-m x 4-m) band transects at each site to quantify density and biomass of parrotfishes (parrotfishes.csv). We also quantified the cover of benthic functional groups using photoquadrats (n=10) placed at 1-m intervals along 10-m transects (n=4 at each site with 1 additional transect with 3 photoquadrats at AQ) running perpendicular to the reef slope at approximately 10-m depth at each site (benthic-cover.csv). In addition to quantifying the total cover of coral at these 5 sites, we also identified corals to the species level to explore differences in coral community composition across sites. Total coral cover was therefore broken down by species as well.

Finally, we conducted foraging observations of 162 unique individuals of the 5 most common parrotfishes across our 5 fringing reef sites: Scarus iseri, Scarus taeniopterus, Scarus vetula, Sparisoma aurofrenatum, and Sparisoma viride. For 3 species (Scarus taeniopterus, Scarus vetula, and Sparisoma viride), we conducted observations of both ontogenetic phases (initial and terminal phase) to investigate ontogenetic differences in foraging. During these foraging observations we video recorded parrotfish behavior and later scored videos, recording all bites taken, the target of those bites (benthic functional groups and bites on feces in the water column), and when coral was bitten, the species of coral targeted was identified (bites.csv). The standard length (cm) of every fish, the total duration of each observation (mins), the time during each video recorded observation that the fish was not visible (mins), and the final follow time (total time - lost time; mins) are also reported for each fish (follow-data.csv). The final follow time (Final.Time) is what we used for analyses of foraging rates. All fish were followed between ~1000-1600 hrs local time in Bonaire (AST, UTC/GMT -4).

Parrotfish assemblages, reef habitat, and predatory coral reef fish data from surveys conducted on the Northern Great Barrier Reef, Australia in September of 2014. The survey included 82 sites across 31 reef structures spanning six degrees of latitude. This dataset contains the main environmental parameters for the 82 sites in this study along with site names, latitudes, and longitudes. These data were published in Johnson et al. (2019).

Additional file 1: Table S1. Results of the permutational ANOVA on the bacterial assemblages according to the sample type (control, predated coral and fish mouth) assessed at Ti and Tf for the mesocosm experiment. Table S2. Results of pair-wise tests on the effect of the sample type on the bacterial assemblages for the mesocosm experiment at Ti and Tf. Table S3. Average relative abundance of the families present in the fish mouths for the mesocosm experiment. Table S4. Average relative abundance of the families present in mechanically wounded corals at Ti for the mesocosm experiment. Table S5. Average relative abundance of the families present in mechanically wounded corals at Tf. Table S6. Average relative abundance of the families present in the predated corals at Ti for the mesocosm experiment. Table S7. Average relative abundance of families present in predated corals at Tf. Table S8. Results of the permutational ANOVA on the bacterial assemblages according to the sample type assessed for field experiment including or not water samples. Table S9. Results of pair-wise tests on the effect of the sample type on the bacterial assemblages for the field experiment. Table S10. Average relative abundance of the families present in the fish mouths for the field experiment. Table S11. Average relative abundance of the families present in naturally unbitten corals in the field. Table S12. Average relative abundance of families present in bitten corals for the field experiment. Table S13. Results of ANOVA and non-parametric tests of the effect of the sample type on alpha diversity metrics (Observed Richness and Shannon-Wiener Index) for the mesocosm experiment at Ti and Tf. Table S14. Results of posthoc tests assessing the effect of the sample type on alpha diversity metrics (Observed Richness and Shannon-Wiener index) for the mesocosm experiment at Ti and Tf. Table S15. Results of ANOVA and non-parametric tests on the effect of the type of sample on alpha diversity metrics (Observed Richness and Shannon-Wiener index) for the field experiment. Table S16. Results of posthoc tests on the effect of the sample type on alpha diversity metrics (Observed Richness and Shannon-Wiener index) for the field experiment. Table S17. Results from differential abundance analyses (DESeq2) on the effect of the sample type at Ti for the mesocosm experiment. Table S18. Average relative abundance of taxa present in greater differential abundance in predated corals compared to mechanically wounded corals for the mesocosm experiment at Ti and Tf. Table S19. Results from differential abundance analyses (DESeq2) on the effect of the sample type at Tf for the mesocosm experiment. Table S20. Differential abundance analysis for the field experiment according to the sampletype. Table S21. Average relative abundance of taxa present in greater differential abundance in naturally bitten corals compared to controls for the field experiment. Table S22. Results of Permutation test for homogeneity of multivariate dispersions (betadisper) on the effect of the sample type in the field survey. Table S23. Results of Permutation test for homogeneity of multivariate dispersion (betadisper) on the effect of the sample type in the field survey. Table S24. filtered unprocessed sOTU table for the mesocosm experiment. Table S25. Taxa table for the negative control of the mesocosm experiment. Table S26. filtered unprocessed sOTU table for the field survey. Table S27. Taxa table for the negative control in the field survey.

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Data associated with the publication 'Ecological drivers of parrotfish coral predation vary across spatial scales', comparing parrotfish coral predation intensity as it relates to parrotfish density/biomass, coral cover, and other ecological variables from the scale of individual coral colonies to reefs spanning four regions of the Greater Caribbean. This dataset includes several datasets: 1) regional_coral_scar_data.csv: Surveys of coral colonies (with and without parrotfish predation scars) across all regions. 2) processed_coral_scar_data_colony_level.csv: Processed data from the file above filtered to only include coral taxa commonly predated by parrotfishes (determined as coral taxa for which at least 3 colonies across the entire dataset had 3 recent parrotfish predation scars). This includes the calculated coral colony surface area and the estimated total/sum recent scar area per coral colony. 3) regional_fish_data.csv: Parrotfish abundance and size for individuals greater than or equal to 15 cm fork length. This data includes estimated fish weight and related length-weight conversion values used to calculate these values. 4) site_coordinates.csv: Metadata of the latitude and longitude of all study sites.

Data collected from manipulative experiments conducted in the Florida Keys. Includes data on algal diversity in fish exclosure plots, reported as total number of unique macroalgal species in each plot. Coral growth data, measured over the course of 14 months. Benthic cover, calculated as the percent cover of canopy and benthos for specific algal groups, and feeding data, presented as the sum of bites taken by scarids and acnathurids of different size classes in exlcosure treatments throughout the experiment.

This dataset contains parrotfish bite observations for the study plots at Pickles Reef, Florida Keys National Marine Sanctuary from 2009-2013. Published in Nature Communications (2016) doi:10.1038/ncomms11833, Supplementary Data 2c.

Natural history of the study site:
This experiment was conducted in the area of Pickles Reef (24.99430, -80.40650), located east of Key Largo, Florida in the United States. The Florida Keys reef tract consists of a large bank reef system located approximately 8 km offshore of the Florida Keys, USA, and paralleling the island chain. Our study reef is a 5-6 m deep spur and groove reef system within this reef tract. The reefs of the Florida Keys have robust herbivorous fish populations and are relatively oligotrophic. Coral cover on most reefs in the Florida Keys, including our site, is 5-10%, while macroalgal cover averages ~15%, but ranges from 0-70% depending on location and season. Parrotfishes (Scaridae) and surgeonfishes (Acanthuridae) are the dominant herbivores on these reefs as fishing for them was banned in 1981. The other important herbivore on Caribbean reefs, the urchin Diadema antillarum, remains at low densities across the Florida Keys following the mass mortality event in 1982-3.

Related Reference:
Zaneveld, J.R., D.E. Burkepile, A.A. Shantz, C. Pritchard, R. McMinds, J. Payet, R. Welsh, A.M.S. Correa, N.P. Lemoine, S. Rosales, C.E. Fuchs, and R. Vega Thurber (2016) Overfishing, nutrient pollution, and temperature interact to disrupt coral reefs down to microbial scales. Nature Communications 7:11833 doi:10.1038/ncomms11833 Supplementary Information

With over 600 valid species, the wrasses (family Labridae) are among the largest and most successful of the marine teleosts. They feature prominently on coral reefs where they are known not only for their impressive diversity in colouration and form, but also in their functional specialization and ability to occupy a wide variety of trophic guilds. Among the wrasses, the parrotfishes (tribe Scarini) display some one of the most dramatic examples of trophic specialization. Using abrasion-resistant biomineralized teeth, parrotfishes are able to mechanically extract protein-rich micro-photoautotrophs growing in and amongst reef carbonate material, a dietary niche that is inaccessible to most other teleost fishes. This ability to exploit an otherwise untapped trophic resource is thought to have played a role in the diversification and evolutionary success of the parrotfishes. In order to better understand the key evolutionary innovations leading to the success of these dietary specialists, we sequenced and analysed the genome of a representative species, the spotted parrotfish (Cetoscarus ocellatus). We find significant expansion, selection, and duplication within several detoxification gene families and a novel poly-glutamine expansion in the enamel protein ameloblastin, and we consider their evolutionary implications. Our genome provides a useful resource for comparative genomic studies investigating the evolutionary history of this highly specialized teleostean radiation.

This dataset contains the digitized treatments in Plazi based on the original journal article Joao Luiz Gasparini, Jean-Christophe Joyeux, Sergio R. Floeter (2003): Sparisoma tuiupiranga, a new species of parrotfish (Perciformes: Labroidei: Scaridae) from Brazil, with comments on the evolution of the genus. Zootaxa 384: 1-14, URL: http://www.zoobank.org/urn:lsid:zoobank.org:pub:82142975-3858-4904-A267-7B549FEBEAF3

The ecological impacts of coral bleaching on reef communities are well documented, but resultant impacts upon reef-derived sediment supply are poorly quantified. This is an important knowledge gap because these biogenic sediments underpin shoreline and reef island maintenance. Here we explore the impacts of the 2016 bleaching event on sediment generation by two dominant sediment producers (parrotfish and Halimeda spp.) on southern Maldivian reefs. Our data identifies two pulses of increased sediment generation in the three years since bleaching. The first occurred within ~6 months after bleaching as parrotfish biomass and resultant erosion rates increased, likely in response to enhanced food availability. The second pulse occurred 1-3 years post-bleaching, after further increases in parrotfish biomass and a major (~4-fold) increase in Halimeda spp. abundance. Total estimated sediment generation from these two producers increased from ~0.5 kg CaCO3 m-2 yr-1 (pre-bleaching; 2016) to ~3.7 kg CaCO3 m-2 yr-1 (post-bleaching; 2019), highlighting the strong links between reef ecology and sediment generation. However, the relevance of this sediment for shoreline maintenance likely diverges with each producer group, with parrotfish-derived sediment a more appropriate size-fraction to potentially contribute to local island shorelines. Methods Benthic cover data was collected along replicate 10 m transects (n= 5) in January and September 2016, March 2017 and January 2019, from the south-western margins of five uninhabited atoll interior reefs in Gaafu Dhaalu atoll, southern Maldives. All data were collected from sites along the outer reef flat/upper reef front (~2 m depth contour) using the ReefBudget methodology. Recorded groups included scleractinian corals to the genera and morphological level e.g., Acropora branching, Porites massive etc.; crustose coralline algae (CCA); turf algae; fleshy macroalgae; Halimeda spp.; sediment; rubble; and other benthic organisms. All data were collected as a function of the true 3-dimensional surface of the reefs, thus including cover on overhangs and vertical surfaces.

Parrotfish abundance (ind. ha-1) was quantified via underwater visual census (UVC) along eight 30 m x 4 m belt transects in the same region of each reef in each time period, with all surveys completed by the same experienced observer (K.M.M.). Details on parrotfish species, life phase (juvenile, initial and terminal) and total length (in size classes of 10 cm) were recorded for each individual. Parrotfish biomass (kg ha-1) for each species and size class was then calculated using established length-weight relationships and multiplied by fish abundance, following the approach described in: Januchowski-Hartley FA, Graham NA, Wilson SK, Jennings S, Perry CT. (2017) Drivers and predictions of coral reef carbonate budget trajectories. Proc Royal Soc B. 284:20162533 (doi.org/10.1098/rspb.2016.2533)

This is the dataset used for the Yarlett et al. (2021) article "Quantifying production rates and size fractions of parrotfish-derived sediment: a key functional role on Maldivian coral reefs" published in Ecology and Evolution.

Resolving how species compete and coexist within ecological communities represents a long-standing challenge in ecology. Research efforts have focused on two predominant mechanisms of species coexistence: complementarity and redundancy. But findings also support an alternative hypothesis that within-species variation may be critical for coexistence. Our study focuses on nine closely related and ecologically similar coral reef fish species to test the importance of individual- versus species-level traits in determining the size of dietary, foraging substrate, and behavioural interaction niches. Specifically, we asked: (i) What level of biological organization best describes individual-level niches? (ii) How are herbivore community niches partitioned among species, and are niche widths driven by species- or individual-level traits? Dietary and foraging substrate niche widths were best described by species identity, but no level of taxonomy explained behavioural interactions. All three niches were dominated by only a few species, contrasting expectations of niche complementarity. Species- and individual-level traits strongly drove foraging substrate and behavioural niches, respectively, whereas the dietary niche was described by both. Our findings underscored the importance of species-level traits for community-level niches, but highlight that individual-level trait variation within a select few species may be a key driver of the overall size of niches.

in situ visual surveys of reproductive behavior, spawning and courtship events

During ontogeny, animals often undergo significant shape and size changes, coinciding with ecological shifts. This is evident in parrotfishes (Eupercaria: Labridae), which experience notable ecological shifts during development, transitioning from carnivorous diets as larvae and juveniles to herbivorous and omnivorous diets as adults, using robust beaks and skulls for feeding on coral skeletons and other hard substrates. These ontogenetic shifts mirror their evolutionary history, as parrotfishes are known to have evolved from carnivorous wrasse ancestors. Parallel shifts at ontogenetic and phylogenetic levels may have resulted in similar evolutionary and ontogenetic allometric trajectories within parrotfishes. To test this hypothesis, using micro-CT scanning and 3D geometric morphometrics, we analyze the effects of size on the skull shape of the striped parrotfish Scarus iseri and compare its ontogenetic allometry to the evolutionary allometries of 57 parrotfishes and 162 non-parrotfish..., To investigate growth allometry, we examined the ontogenetic series of S. iseri, encompassing 54 individuals with a total length ranging from 1.75 to 33.5 cm. For skull shape comparison analyses among S. iseri, other parrotfishes, and non-parrotfishes wrasses, our sample of adults comprises 336 individuals (160 adult parrotfishes and 176 adult non-parrotfish wrasses) from 217 labrid fishes (Table S1). From this dataset, we compared the evolutionary allometry of Scarines reef clade (57 species) to ontogenetic allometry of S. iseri. The ontogenetic series of S. iseri was obtained through sampling carried out in Belize in 2023 (IACUC protocols: UT Austin/AUP-2021-00064 and SERC/10-15-15-SJB; Collection permits: BF000005-16 and BF0042-22) with additional individuals from the Field Museum of Natural History (FMNH). The remaining species were obtained through several museums (Table S1). We assessed the three-dimensional skull shape of each labrid species through micro-computed tomography (μC..., , # Ecological shifts underlie parallels between ontogenetic and evolutionary allometries in the striped parrotfish

Continued methods

(a)Â Â Ontogenetic allometry of *Scarus iseri*

To analyze the shape variation of entire skull and individual bones of S. iseri across development, we applied Principal Component Analysis (PCA) using gm.prcomp function in geomorph package (Adams et al., 2022).

To estimate coefficients of ontogenetic allometry and test the effects of size on skull and bone shapes (superimposed coords), we used Analysis of Variance, fitting a model with one main effect, the factor “Size†, measured as ln-transformed CS (LCS). The ANOVA was performed using the procD.lm function in geomorph (Collyer and Adams, 2018; 2021). To better visualize these relationships, we predicted individual shapes using group-specific regression models, and the resulting shapes for all samples were plotted using a PCA. We plotted PC1 scores against size. Allometric axes were then plo...

Species-specific projected total habitat suitability index (HSI) and HSI's change or 'anomaly' under different carbon dioxide emission levels, including (A) total HSI for the 1970 to 2000 period; and changes in HSI under scenarios of (B) ~400 ppm and (C) ~565 ppm atmospheric carbon dioxide concentration in the high resolution Earth system model (GFDL CM2.6).

Stoplight parrotfish and queen parrotfish eye lens core validation samples.

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