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495 results for “Reef Fishes”
Species ecology explains the various spatial components of genetic diversity in tropical reef fishes
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Weak integration allows novel fin shapes and spurs locomotor diversity in reef fishes
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Multi-decadal stability of fish productivity despite increasing coral reef degradation
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Data from: The role of fish feces for nutrient cycling on coral reefs
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Data from: Regional-scale disturbances drive long-term decline of inshore coral reef fish assemblages in the Great Barrier Reef Marine Park
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Data from: Population genomics, local adaptation, and cryptic speciation in a temperate reef fish, the black surfperch, <em>Embiotoca jacksoni</em>, using genome-wide resequencing
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Data from: Dietary resilience of coral reef fishes to habitat degradation
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Environmental DNA highlights the influence of salinity and agricultural run-off on coastal fish assemblages in the Great Barrier Reef region
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Santa Barbara Channel Coastal and Island fish survey from the Reef Check, 2006-2017
The data were collected by the Reef Check organization: https://reefcheck.org/ Every year, Reef Check trains thousands of citizen scientist divers who volunteer to survey the health of coral reefs around the world, and rocky reef ecosystems along the entire coast of California. The programs monitor rocky reefs inside and outside of California's marine protected areas (MPAs). The results are used to improve the management of these critically important natural resources. The data presented here were a subset of the data that cover the Santa Barbara Channel region, southern California, USA.
SONGS Mitigation Monitoring: Experimental Reef Survey – Fish Size and Abundance
These data describe annual estimates of the size and abundance of reef fish at an artificial reef (Wheeler North Reef in Orange County, CA) and two natural reference reefs (San Mateo Kelp in Orange County, CA and Barn Kelp in San Diego County, CA). Data were collected from 2000 to 2004 as part of the experimental phase of the San Onofre Nuclear Generating Station (SONGS) kelp reef mitigation program. In the summer of each year, divers identified, sized, and counted species of fish along fixed transects and in quadrats uniformly distributed at each reef.
UCSB SONGS Mitigation Monitoring: Reef Survey - Fish Fecundity, Feeding, and Somatic Growth
These data describe annual estimates of the fecundity, gut fullness, and somatic growth of five fish species at three subtidal reefs collected as part of the San Onofre Nuclear Generating Station (SONGS) Mitigation Monitoring Program. Data collection began in 2009 at an artificial reef (Wheeler North Reef in Orange County, CA) and two natural reference reefs (San Mateo Kelp in Orange County, CA and Barn Kelp in San Diego County, CA). Fish were collected annually at each reef between May and October.
MCR LTER: Coral Reef: Changes in the abundance of fish functional groups: Adam et al. 2014 Oecologia
These data were generated from two long-term time series (knb-lter-mcr.4 and knb-lter-mcr.6) in order to analyze the relationship between the cover of live and dead branching corals and changes in the abundance of different functional groups of fishes following the loss of coral on the fore reef of Moorea due to an outbreak of corallivorous crown-of-thorns sea stars (Acanthaster planci) and a tropical cylcone. Analyses were conducted in support of an ecological manuscript published in Oecologia Adam, T. C., Brooks, A. J., Holbrook, S. J., Schmitt, R. J., Washburn, L., Bernardi, G. How will coral reef fish communities respond to climate-driven disturbances? Insight from landscape-scale perturbations. Global climate change is rapidly altering disturbance regimes in many ecosystems including coral reefs, yet the long-term impacts of these changes on ecosystem structure and function are difficult to predict. A major ecosystem service provided by coral reefs is the provisioning of physical habitat for other organisms, and consequently, many of the effects of climate change on coral reefs will be mediated by their impacts on habitat structure. Therefore, there is urgent need to understand the independent and combined effects of coral mortality and loss of physical habitat on reef-associated biota. Here, we use a unique series of events affecting the coral reefs around the Pacific island of Moorea, French Polynesia to differentiate between the impacts of coral mortality and the degradation of physical habitat on the structure of reef fish communities. We found that by removing large amounts of physical habitat, a tropical cyclone had larger impacts on reef fish communities than an outbreak of coral-eating sea stars that caused widespread coral mortality but left the physical structure intact. In addition, the impacts of declining structural complexity on reef fish assemblages accelerated as structure became increasingly rare. Structure provided by dead coral colonies can t
MCR LTER: Coral Reef: Community Dynamics: Physical Characteristics of Branching Acropora Patches and Species Richness and Abundances of Associated Fishes
Branching corals, like many in the genus Acropora, provide structurally complex habitats for reef fishes and other organisms. Fluctuations in the abundance, distribution and characteristics of staghorn Acroporid corals may contribute to changes in the abundance and species composition of reef fishes due to changes in the availability of shelter habitat and food. Farming damselfishes of the genus Stegastes occur in high abundances in staghorn thickets and actively defend food and nest space against organisms that threaten these resources. Here I examine the value of staghorn thickets as habitat for fishes, and how the presence of territorial farming damselfishes may influence the assemblage of fishes that associate with staghorn corals. Surveys of 185 Acropora pulchra thickets located in the lagoons surrounding the island of Moorea, French Polynesia revealed 85 species of fish from 25 families. Total fish abundance and species richness values ranged from no fish on a thicket to a high of 275 individuals and 26 species. Thicket area was the most important characteristic in explaining variation in attributes of the fish assemblage among staghorn thickets, with other characteristics explaining little of the species composition or trophic structure. Behavioral observations revealed that farming damselfishes were most aggressive toward corallivores, herbivores, and egg predators, while they ignored most carnivores and omnivores. Despite this pattern, I observed positive covariance between Stegastes and the group of fishes that elicited the strongest aggressive response when the effect of thicket area was removed, suggesting these fishes remain drawn to the resources produced or enhanced by Stegastes on A. pulchra thickets.
Data from: A closer examination of the 'abundant center' hypothesis for reef fishes
<p>Aim: The 'abundant center' hypothesis states that species are more abundant at the center of their range. However, several recent large-scale studies have failed to find evidence for such a pattern. Here we use extensive global data of reef fishes to test the strength of the 'abundant center' pattern, and to examine variation in the patterns across species using life history and ecological traits.</p> <p>Location: Marine habitat at a global extent: from Indo-Pacific to Atlantic reefs.</p> <p>Methods: We used underwater visual estimates of fish abundance, containing 22,963 transects and 1,215 species. For each species we calculated the slope between abundance and distance to the range center, with the range center estimated using four different methods. We tested whether abundance patterns differ between the range core and margins using segmented regression. Meta-analytic methods were used to synthesize results across species, and to test whether species traits can explain variation in the fit to the pattern among species.</p> <p>Results: The method used to define the range center had a large effect on the results. Nevertheless, in all cases we found large variation between species. Results of the segmented regression revealed that changes in abundance across the range core are very small and that steep declines in abundance happen only toward the range margins. Body size and mean abundance were the main traits affecting the fit to the pattern across species.</p> <p>Main conclusions: We find large variation across species in the fit to the abundance center pattern. Nevertheless, we do find support for a general pattern of a range core with high, but variable, abundance and steep decline in abundance toward the range periphery. Thus, species do tend to be rare at the range margins, making then sensitive to extirpation due to both natural and anthropogenic impacts.</p>
Dominance of endemics in the reef fish assemblages of the Hawaiian Archipelago
<p>Aim: Species ranges provide a valuable foundation for resolving biogeographic regions, evolutionary processes, and extinction risks. To inform conservation priorities, here we develop the first bioregionalization based on reef fish abundance of the Hawaiian Archipelago, which spans nearly 10° of latitude across 2,400 km, including 8 high volcanic islands in the populated main Hawaiian Islands (MHI), and 10 low islands (atolls, shoals, and islets) in the remote northwestern Hawaiian Islands (NWHI)..</p> <p>Location: The Hawaiian Archipelago.</p> <p>Taxon: Fishes (276 taxa).</p> <p>Methods: We compiled 5,316 visual fish surveys at depths of 1-30 m from throughout the Hawaiian Archipelago. Geographic range (km2) for each species was measured as extent of occurrence (EOO) and area of occurrence (AOO). PERMANOVA and PCO were used to investigate drivers of fish assemblage structure. Distance-based multivariate analyses were used to evaluate the relationship between fish assemblage structure and predictor variables including latitude, reef area, temperature, chlorophyll-a, wave-energy, and human population density.</p> <p>Results: Distinct fish assemblages exist in the MHI and NWHI, with two additional faunal breaks driven primarily by endemic species abundance. Latitude explained 37% of the variability in fish assemblages, with reef area accounting for an additional 9%. EOO showed a significant correlation with latitude. Endemics comprised 52-55% of the numerical abundance at the northern end of the archipelago but only 17% on Hawai'i Island in the extreme south. Maximum size and activity regime (day vs. night) explained the most variation in the abundance of endemics.</p> <p>Main conclusions: The Hawaiian fish assemblages are strongly influenced by endemic species, affirming the archipelago as a biodiversity hotspot of high conservation value. The higher abundance of endemics in the NWHI may represent preadaptation to oceanic (oligotrophic) conditions. Resolution of distinct bioregions across the archipelago provides a better understanding of reef fish macroecology, with implications for management at the archipelago scale.</p>
Data from 'Planktivores as trophic drivers of global coral reef fish diversity patterns'
<p>Datasets and scripts generated in the paper 'Planktivores as trophic drivers of global coral reef fish diversity patterns', published in PNAS. More details can be found in the README file.</p>
Data from: Diet reveals links between morphology and foraging in a cryptic temperate reef fish
Predators select prey so as to maximize energy and minimize manipulation time. In order to reduce prey detection and handling time, individuals must actively select their foraging space (microhabitat) and populations exhibit morphologies that are best suited for capturing locally available prey. We explored how variation in diet correlates with habitat type, and how these factors influence key morphological structures (mouth gape, eye diameter, fin length, fin area, and pectoral fin ratio) in a common microcarnivorous cryptic reef fish species, the triplefin Helcogrammoides cunninghami. In a mensurative experiment carried out at six kelp-dominated sites, we observed considerable differences in diet along 400 km of the Chilean coast coincident with variation in habitat availability and prey distributions. Triplefins preferred a single prey type (bivalves or barnacles) at northern sites, coincident with a low diversity of foraging habitats. In contrast, southern sites presented varied and heterogeneous habitats, where triplefin diets were more diverse and included amphipods, decapods, and cumaceans. Allometry-corrected results indicated that some morphological structures were consistently correlated with different prey items. Specifically, large mouth gape was associated with the capture of highly mobile prey such as decapods, while small mouth gape was more associated with cumaceans and copepods. In contrast, triplefins that capture sessile prey such as hydroids tend to have larger eyes. Therefore, morphological structures co-vary with habitat selection and prey usage in this species. Our study shows how an abundant generalist reef fish exhibits variable feeding morphologies in response to the distribution of potential habitats and prey throughout its range.
Data from: Differential persistence favors habitat preferences that determine the distribution of a reef fish
A central focus of population ecology is understanding what factors explain the distribution and abundance of organisms within their range. This is a key issue in marine systems, where many organisms produce dispersive larvae that develop offshore before returning to settle on benthic habitat. We investigated the distribution of the neon goby, Elacatinus lori, on sponge habitat and evaluated whether variation in the persistence of recently settled individuals (i.e., settlers) among different sponge types can result in habitat preferences and establish their observed distribution. We found that E. lori settlers were more likely to occur on large yellow tube sponges (Aplysina fistularis) than on small yellow sponges or brown tube sponges (Agelas conifera). An experiment seeding settlers onto multiple species and sizes of sponge habitat revealed that settlers persist longer on large yellow sponges than on small yellow sponges or brown sponges. Habitat preference experiments also indicated that settlers prefer large yellow sponges over small yellow sponges or brown sponges. Settlers achieved these preference behaviors using visual, but not chemical, cues. Finally, new settlers arriving from the water column were more likely to occur on large yellow sponges than on small yellow sponges or brown sponges, indicating that the observed habitat preferences existed independent of prior experience. These results support the hypothesis that E. lori have evolved behavioral preferences for sponge habitats that will maximize their post-settlement persistence, and that decisions at settlement will shape the population level pattern of settler distribution on coral reefs.
Bermuda Reef Ecosystem Assessment and Mapping Programme: Baseline Coral Reef and Fish data
<p>BREAM: Bermuda Reef Ecosystem Analysis and Mapping Programme, mapped all coral reefs across the Bermuda platform in 2003. We then surveyed over 200 sites for benthic and fish assemblages using the AGRRA.org v4 methods, with local modifications. See www.bermudaBREAM.org for more information about the baseline monitoring work, or to contact us for additional data and information.</p> <p>Contributors:</p> <p>Research Associates:</p> <p>Jessie Murdoch MSc; Robert Fisher, BFA; Gretchen Goodbody-Gringley, PhD, Matthew Strong BSc; Struan R. Smith PhD</p> <p>Undergraduate Interns</p> <p>Taylor Gorham, Anke Moesinger, Molly Sinnott, D’mitri Williams</p> <p>Graduate Interns</p> <p>Gerardo Toro-Farmer, Mike Colella, Brittany Huntington, Katherine Yates</p> <p>Volunteers</p> <p>Ian Murdoch; Judie Clee; Teddy Gosling; Gil Nolan; Lynn Wolfe</p> <p>RV Endurance Captain: Tim Hasselbring</p> <p> </p>
Reef-associated Bony Fishes of the Greater Caribbean: A Checklist (VERSION 5)
<p><strong> Reef-associated Bony Fishes of the Greater Caribbean: A Checklist (VERSION 5)</strong></p><p> </p><p> Date: November 30, 2023 <strong>DOI 10.5281/zenodo.10225031</strong></p><p> https://zenodo.org/records/10225031</p><p><strong>D Ross Robertson</strong> </p><p>Smithsonian Tropical Research Institute, Balboa, Republic of Panama. <a href="mailto:Robertsondr@si.edu">Robertsondr@si.edu</a> </p><p><strong>Luke Tornabene</strong> </p><p>School of Aquatic and Fishery Sciences, and the Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98105, U.S.A. <a href="mailto:Luke.Tornabene@gmail.com">Luke.Tornabene@gmail.com</a></p><p><strong>Introduction to the Fifth Edition</strong></p><p><strong>Changes to this edition include:</strong> <strong>1.</strong> Rearrangements of species in different families following splitting up of some families (e.g. Cyclopsettidae split off from Paralichthyidae; Spratelloididae split off from Clupeidae) and reassignment of some genera from one family to another (e.g. <i>Peristedion</i> has been reassigned to Triglidae) following changes defined in Eschmeyer's Catalog of Fishes. 2. Some previously undescribed species in version four have been described and named (e.g. <i>Polylepion species 1</i> is now <i>Polylepion gilmorei</i>). <strong>3. </strong>Some species have been reclassified as reef associated based on additional information on habitat usage, photographs of fishes in natural habitat, such as those on iNaturalist (<a href="https://inaturalist.org">https://inaturalist.org</a> ) and information on collection habitat (e.g. <i>Gillellus inescatus</i>). <strong>4.</strong> Some species have been reclassified as non-endemic to the región, based on new information about occurrence in Brazil (e.g. <i>Cephalopholis cruentatus</i>), while others have been reclassified as endemics to the región based on taxonomic splits (e.g. <i>Pareques acuminatus, Sphoeroides spengleri</i>). <strong>5.</strong> A few newly described, resurrected or otherwise recognized species (e.g. <i>Rhonciscus paucus</i>, <i>Pareques lineatus, Sphoeroides camila</i>) have been added to the list.</p><p><strong>Note:</strong> All changes and new data in the list are indicated in <strong>red </strong>and all reef-associated species have their <strong>names highlighted</strong> for ease of recognition. Also note the explanatory <strong>text added</strong> to the introduction to the Fourth Edition, below.</p><p> </p><p>I<strong>ntroduction to the Fourth Edition</strong></p><p>This fourth edition of the checklist includes bony fishes belonging to families present in the Greater Caribbean biogeographic region that have species known to associate with shallow (0 – 40 m depth) coral and rocky reefs. That region extends from Cape Hatteras in the southeastern USA, through the Gulf of Mexico and the Caribbean Sea to somewhere around Guyana and includes the West Indies and Bermuda. </p><p>The classification of families and spelling of scientific names generally follows Eschmeyer's Catalog of Fishes. (<a href="https://www.calacademy.org/scientists/projects/eschmeyers-catalog-of-fishes">https://www.calacademy.org/scientists/projects/eschmeyers-catalog-of-fishes</a></p><p>The objective of this checklist is to provide a database of the entire regional fauna of reef-associated bony fishes that includes information on its taxonomic composition, and the conservation (IUCN Red List) status and various ecological characteristics of listed species. This is intended to facilitate comparisons of the structure of equivalent regional faunas in different parts of the globe, and for examining local variation in faunal structure (and faunal inventories) within the Greater Caribbean. Over the past decade the <strong>IUCN Red List</strong> (<a href="https://www.iucnredlist.org/">https://www.iucnredlist.org/</a>) has produced a comprehensive set of assessments of Greater Caribbean fishes. Those include assessments for >95% of the species in the present checklist. Those assessments include much information on habitat usage by those fishes that was relevant to the construction of the present checklist. That information was supplemented with information from our own research and other published sources. Many of the reef-associated fishes known from the Greater Caribbean also occur in Brazil. <strong>Those non-endemics are considered to be residents in the Greater Caribbean if there are multiple records of them in that region, particularly records in different years and at different locations. However, species that associate with reefs in Brazil do not necessarily do so in the Greater Caribbean; </strong><i><strong>Mola mola</strong></i><strong> is an example.</strong> Information used here was extracted from 185 publications about Greater Caribbean reef-<strong>associated </strong>fishes and 152 publications on Brazilian reef-<strong>associated</strong> fishes.</p><p>Greater Caribbean reefs down to depths of ~250-300 m have reef-fish faunas dominated by members of typical shallow-reef families of bony fishes (Baldwin et al. 2018). Here we focus exclusively on species belonging to those families, because those are what are traditionally considered to be reef fishes. In the Greater Caribbean this reef-fish fauna includes 992 species of native fishes belonging to 342 genera and 84 families, 92% of which are demersal or benthic forms, and 8% pelagic species. </p><p>Members of a few families of bony fishes that are found only on deep-water reefs (i.e. typically below the 150 m lower limit of the mesophotic zone) and have no representatives that live on shallow reefs, are not included here: Acropomatidae, Anomalopidae, Aulopidae, Berycidae, Caproidae, Gempylidae, Grammicolepidae, Polymixiidae, Polyprionidae, Scombropidae, Sebastidae, Setarchidae, Symphysanodontidae, Trachichthyidae, and Triacanthodidae. Between them those 14 families have a total of ~43 species in the Greater Caribbean, only some of which are known to associate with very deep reefs.</p><p>The list is restricted to native species and excludes introduced non-native species with resident populations in the Greater Caribbean, notably <i>Pterois volitans</i> and <i>Neopomacentrus cyanomos</i>.</p><p><i><strong>Reef-associated fishes</strong></i> include not only <strong>demersal and benthic species that use consolidated hard substrata</strong> (coral- and rocky reefs) but also <strong>demersal and benthic species that use soft bottoms</strong> (sand, gravel, mud, seagrass and macroalgal beds growing on sediment, estuaries and mangroves) immediately adjacent to or within the matrices of reefs. <strong>Benthic</strong> species are restricted to living on and in the bottom, whereas <strong>Demersal</strong> species use and rely on both the bottom and the near-bottom water column. <strong>These two categories both relate to the behavior of fishes during the day,</strong> which, in some cases, changes at night. For example, Apogonids and Holocentrids are benthic during the day, but demersal when they become active at night, and day-active demersal species often hide within reef substrata at night (e.g. some <i>Thalassoma bifasciatum</i> rest inside tubular sponges, while <i>Halichoeres bivittatus</i> buries in sand). Reef-associated fishes also include <strong>Pelagic species</strong> that live in the water column, facultatively associate with reefs, are regularly seen over and immediately adjacent to them, <strong>and have trophic interactions with organisms on reefs, either contributing food to reefs (e. g. parasites removed from pelagic fishes such as jacks by reef fishes) or extracting food from them (e. g. by pelagics such as mackerels (</strong><i><strong>Scomberomorus</strong></i><strong>) preying on spawning reef fishes).</strong></p><p>Oyster reefs are estuarine and have an associated estuarine bony-fish fauna (e. g. see Harding & Mann 2001; La Peyre et al. 2019) that differs greatly in taxonomic composition from the faunas of marine reefs. Hence, we have not included species that associate with oyster reefs unless they also associate with rocky- or coral reefs. Species found almost exclusively in fresh- to brackish water also are excluded entirely from the list. Finally, we also exclude a few taxa of oceanic shallow-water fishes that may be seen in the general vicinity reefs: Exocoetidae, Xiphiidae, Istiophoridae and large (<i>Thunnus)</i> tunas. </p><p><i><strong>Cryptobenthic fishes</strong></i> are species that are "visually and/or behaviorally cryptic" due to their form and coloration, and to their maintaining "a close association with the benthos" (Depczynski & Bellwood, 2003), by living directly on or within it. While cryptobenthic species are a major component of the diversity of reef fishes, they are strongly under-represented in visual surveys of reef-fish assemblages made by divers. The diversity and the numerical abundance of cryptobenthic fishes is revealed only through the use of chemical piscicides (Ackerman & Bellwood 2000; Willis 2001; Smith-Vaniz et al. 2006; Robertson & Smith-Vaniz 2008; Alzate et al. 2014,) or anaesthetics (Kovacic et al. 2012; Robertson & Smith-Vaniz 2010) that flush such fishes out of the substratum for collection and identification. The list indicates which species we have classed as cryptobenthic. While individuals of some cryptobenthic species, such as Muraenids and Apogonids may regularly be seen during the day on reefs while hiding in the substratum, we do not know what fraction of their populations those visible individuals represent (Willis 2001; Alzate et al 2014). On the other hand, species such as the tiny Glass- and Masked Gobies (<i>Coryphopterus hyalinus </i>and<i> C. personatus</i>) that school in the water just above the substratum, and the Garden Eels (<i>Heteroconger spp.</i>) that extend their long, slender bodies to feed in the water column above their burrows, we do not class as cryptobenthic because they can be censused visually. </p><p>Studies of cryptobenthic reef-fishes often emphasize that many such species derive their crypticity in part from being very small (Miller 1979; Depczynski and Bellwood 2003; Beldade et al 2006; Kovacic et al 2012; Brandl et al 2018). The list indicates <strong>which cryptobenthic reef-fishes are small,</strong> with a maximum Total Length (TL) </= 5 cm (Depczynski & Bellwood, 2003) and </= 10 cm (Miller 1979; Beldade et al 2006; Kovacic et al 2012). Brandl et al. (2018, 2019) classed the members of 17 families (only 13 of which are in the Greater Caribbean) that have relatively large numbers of small, cryptobenthic species, share many life-history characteristics and are important for energy flow in reef ecosystems as <strong>Core families of Cryptobenthic Reef-fishes (Core CRFs)</strong>. Members of those families (Apogonidae, Blenniidae, Bythitidae, Callionymidae, Chaenopsidae, Dactyloscopidae, Gobiidae, Gobiesocidae, Grammatidae, Labrisomidae, Opistognathidae, Syngnathidae, Tripterygiidae), which Brandl et al. (2018, 2019) also referred to as <strong>microbenthic reef fishes,</strong> are identified in the list. Shortly before Brandl et al (2018) defined the group of Core CRFs, Moller et al (2016) split the Bythitidae into two families, Bythitidae and Dinematichthyidae. We have included both those families as Core CRFs as both have small, cryptobenthic species found on shallow reefs. While many cryptobenthic species in other families also are small, Brandl et al's. (2018) definition of core CRFs was aimed at the family level, thus excluding some small cryptic species in speciose families that have many large, mobile members (e. g. the Labridae and Serranidae). </p><p><i><strong>Shallow- and deep-reef fishes</strong></i>: Shallow-water species we consider to be those with populations restricted to or concentrated at depths above 40m. Deep-reef species are members of the same shallow-reef families that have populations concentrated in or restricted to depths greater than 40m. This depth breakpoint corresponds to the approximate breakpoint between shallow and deeper (mesophotic and altiphotic) faunal depth-zones on reefs, and the approximate depth breakpoint between research on shallow-water reef fishes based on open-circuit SCUBA, and research at greater depths that rely on mixed gas and Closed-Circuit Rebreather (CCR) technical diving (e.g. Pinheiro et al 2016; Baldwin et al 2018; García-Hernández et al 2018; Stefanoudis et al 2019). <strong> </strong>We classified as shallow some species that have shallow populations at some sites in the Greater Caribbean and deep populations in others (e. g. <i>Gramma melacara</i>), and others in which juveniles are common in shallow water and adults are restricted to deep water (e. g. <i>Lutjanus buccanella</i>). </p><p>Simple systems of habitat characterization like those used here cannot capture all the nuances of how different fishes use a variety of habitats and microhabitats. Inevitably there are borderline cases of species that could be classified in either of two alternative habitat categories (e. g. benthic or demersal, deep or shallow). There also are borderline cases relating to whether a species should be regarded as reef-associated or not. A single observation of a species passing nearby during a dive on a reef does not make that a reef-associated species. In addition, geographic variation in whether some species on this list do or do not associate with reefs at any location complicates the situation. We have tried to be conservative in classing species as reef-associated, by relying as much as possible on multiple primary records of such behavior by those species and clearcut descriptions of actual behavior. Otherwise virtually everything could end up classed as reef associated.</p><p><strong>CHANGES IN VERSION 4 FROM VERSION 3:</strong></p><ol><li>Based on additional information about which species associate with reefs, as well as taxonomic rearrangements, the numbers of taxa on Version 4 of the list changed to <strong>84 Families, 342 Genera and 992 Species, </strong>from 83 Families, 338 Genera and 981 Species in Version 3.</li><li>All species names now have the associated description authority.</li><li>Names of taxa added and of species that have been renamed or re-classified as reef associated in this version are indicated in <strong>BOLD RED.</strong></li><li>The family Malacanthidae traditionally has comprised two subfamilies, the Latilinae and Malacanthinae, with the former including only deep living species in the Greater Caribbean. Those two were recently raised to families. Because of the sister relationship between those to taxa and their previous status we continue to include both among the GC reef-associated fauna.</li><li>The family Anomalopidae was removed from the list because its single Greater Caribbean member is cryptobenthic in deep water during the day, and daytime activity and depth range is the focus of this list (see above). Unlike the situation with the Malacanthids the near relatives of the Anomalopids are all deep-water taxa.</li></ol><p><strong>CHANGES IN VERSION 3 FROM VERSION 2</strong></p><ol><li>This edition incorporates data from additional published research on fishes in the Greater Caribbean, plus information on species that occur in Brazil as well as the Greater Caribbean that we reviewed in ~70 publications that deal with reef-associated fishes in Brazil. That additional information has increased the number of reef-associated bony fishes: to 83 families, 338 genera and 981 species.</li><li>Shortly before Brandl et al (2018) defined the group of Core CRFs, Moller et al (2016) split the Bythitidae into two families, Bythitidae and Dinematichthyidae. In this edition we have included both those families as Core CRFs as the dinematichthyids include many small, cryptobenthic species found on shallow reefs.</li><li>Three additional types of data are given for each species on the list. These include (1) whether or not a species is <strong>endemic </strong>to the Greater Caribbean (i.e has 90% or more of its range within that area, the northern and southern limits of which have yet to be precisely defined), and (2) whether or not it has a <strong>small or very small geographic range</strong> within that region. Small ranges are those no larger than 1/3 of the Greater Caribbean. Very small ranges are those no larger than the area occupied by the Mesoamerican reef system, which extends from northern Honduras and along the Caribbean coast of Mexico and represents ~5% of the area of the Greater Caribbean. Species for which insufficient information is available on range size, but which seem likely to have small ranges, are indicated with a query. Note that non-endemics can have small Greater Caribbean ranges that represent part of larger ranges that extend well outside that region, e.g. to Brazil. (3) The <strong>IUCN Red List extinction-risk category</strong> is also given for each species that has been assessed by that process. Red List categories include DD (Data Deficient); LC (Least Concern); NT (Near Threatened); VU (Vulnerable); E (Endangered); CR (Critically Endangered). Species not yet assessed by the Red List are indicated by ND (no data).</li></ol><p> </p><p><strong>CHANGES IN VERSION 2 FROM VERSION 1:</strong></p><ol><li>In Version 1 all non-pelagic species were referred to as demersal. In Version 2 non-pelagic species are coded as either <strong>Benthic</strong> or <strong>Demersal </strong>(see above for definitions<i>). </i></li><li>Species have been divided into <strong>two depth classes</strong>, based on their depth ranges: <strong>Shallow species</strong> are those commonly found above 40m depth and <strong>Deep Species</strong> are those entirely or largely restricted to depths below 40m. The choice of this 40 m separation depth was based on it being the approximate lower limit of SCUBA-based research on shallow-water reef fishes, and also being the approximate breakpoint between shallow and deeper (mesophotic and rariphotic) faunal depth-zones on reefs, with shallow- and deep-reef fish assemblages being dominated by different members of the same set of families indicated in the table presented here (e.g. Pinheiro et al 2016; Baldwin et al 2018; García-Hernández et al 2018; Stefanoudis et al 2019).</li></ol><p> </p><p>This division into shallow- and deep species was made because levels of research effort on deep-reef members of the families on the list vary widely between regions and between locations within a region. There has been much more research and collecting of deep-reef fishes, particularly of small, cryptobenthic forms, using crewed submersibles specially equipped for such collecting (Gilmore 2016) in the Greater Caribbean than many other areas. That includes work at widely scattered sites in the region between the late 1970s and 2010 by the <strong>Johnson Sea Link I</strong> and <strong>II</strong> submarines, on the Atlantic and Gulf of Mexico coasts of Florida, the Bahamas, Caribbean Mexico, Cuba, Jamaica, Puerto Rico, the US Virgin Islands, Bonaire and Curacao. In addition, this activity includes observations by the <strong>Nekton</strong> submersibles at Jamaica and Belize, and the <strong>Alvin</strong> at the Bahamas (again during the 1970s). During the 2010s, this effort was renewed by observations and collecting by the Smithsonian Institution's DROP program using the submersibles <strong>Curasub</strong> at Curacao, Bonaire, Dominica and St Eustatius, and the <strong>Idabel</strong> at Roatan. No similarly extensive set of submersible-based studies and collections of deep-reef fishes exists for any other equivalent biogeographic region in the tropics. Hence, the focus of quantitative comparisons with reef-associated fish faunas of most other regions (or locations within the Greater Caribbean that lack deep-reef research) is likely to be on shallow-water reefs.</p><p> </p><ol><li>A few, currently unnamed species of reef-associated Gobiids (6 species in two, currently unnamed, genera), Grammatids (2 species of <i>Lipogramma</i>), Labrids (2 species of <i>Decodon</i>) and Serranids (1 species of <i>Baldwinella</i>) for which sufficient ecological information is available have been added to the list.</li></ol><p> </p><ol><li>Several deep-living reef-associated species listed in Version 1 as members of the Scorpaenidae have been removed from the list, because systematic rearrangements have placed them in other families (Setarchidae and Sebastidae) that, in the study area, lack shallow members.</li></ol><p> </p><ol><li>The family Ophidiidae has about 78 species in 28 genera and three subfamilies in the study are. We include on the list only 41 members of 7 genera known to have shallow-water, reef-associated representatives or representatives that live within the depth range (0-~250m) of reefs dominated by shallow taxa. The remainder are species that live in very deep or oceanic waters and are irrelevant to the reef-associated fish fauna considered here.</li></ol><p> </p><ol><li>Habitat classifications of a few species of carangids and lutjanids as pelagic or demersal in version 1 have been changed, based on additional information.</li></ol><p> </p><p>Hosting of this database by Zenodo will allow it to be updated through the production of new versions as new information becomes available.</p><p>New information, comments or queries relating to the classification or species list should be directed to <a href="mailto:robertsondr@si.edu">robertsondr@si.edu</a>. </p><p>A compilation of further information about the biological characteristics of fishes on this list can be found in the website: Robertson DR, Van Tassell J (2019) Shorefishes of the Greater Caribbean: online information system. Version 2.0. <a href="https://biogeodb.stri.si.edu/caribbean/en/pages">https://biogeodb.stri.si.edu/caribbean/en/pages</a></p><p> </p><p><strong>References.</strong></p><p>Ackerman JL, Bellwood DR (2000) Reef fish assemblages: a re-evaluation using enclosed rotenone stations <i>Marine Ecology Progress Series</i> 206:227-237. doi:10.3354/meps206227</p><p>Alzate, Zapata FA, Giraldo A (2014) A comparison of visual and collection-based methods for assessing community structure of coral reef fishes in the Tropical Eastern Pacific. <i>Revista Biologica Tropical </i>62 (Supplement 1): 359–371.</p><p>Baldwin CC, Tornabene L, Robertson DR (2018) Below the mesophotic. <i>Scientific Reports</i> 8:4920 DOI:10.1038/s41598-018-23067-1</p><p>Beldade R, Erzini K, Goncalves EJ (2006) Composition and temporal dynamics of a temperate rocky<br>cryptobenthic fish assemblage. <i>Journal of the Marine Biological Association of the U.K. 86: 1221-1228.</i> </p><p>Brandl SJ, Goatley CHR, Bellwood DR, Tornabene L (2018) The hidden half: ecology and evolution of cryptobenthic fishes on coral reefs. <i>Biological reviews of the Cambridge Philosophical Society 93:</i> 1846 -1873. <a href="https://doi.org/10.1111/brv.12423"> https://doi.org/10.1111/brv.12423</a></p><p>Brandl SJ, Tornabene L, Goatley CHR, Casey JM, Morais RA, Côté IM, Baldwin CC, Parravicini<a href="https://science.sciencemag.org/content/364/6446/1189/tab-pdf#aff-5\"""> </a>V, Schiettekatte MD, Bellwood<a href="https://science.sciencemag.org/content/364/6446/1189/tab-pdf#aff-9\"""> </a> DR (2019) Demographic dynamics of the smallest marine vertebrates fuel coral reef ecosystem functioning<i>. Science</i> 364: 1189-1192 DOI: 10.1126/science.aav3384</p><p>Depczynski M, Bellwood DR (2003) The role of cryptobenthic reef fishes in coral reef trophodynamics. <i>Marine Ecology Progress Series</i> 256: 183–191</p><p>García-Hernández JE, Sanchez PJ, Hammerman NM and Schizas NV (2018) Fish, coral, and sponge assemblages associated with altiphotic and mesophotic reefs along the Guánica Biosphere Reserve continental shelf edge, southwest Puerto Rico. <i>Frontiers in Marine Science</i> 5:303. doi:10.3389/fmars.2018.00303</p><p>Gilmore, RG Jr (2016) You can't catch a fish with a robot. <i>Gulf and Caribbean Research</i> 27: ii-xiv DOI: 10.18785/gcr.2701.11</p><p>Harding JM, Mann R (2001) Oyster reefs as fish habitat: opportunistic use of restored reefs by transient fishes. <i>Journal of Shellfish Research</i> 20: 951-959.</p><p>Kovacic M, Patzner RA, Schliewen U (2012) A first quantitative assessment of the ecology of cryptobenthic fishes in the Mediterranean Sea. <i>Marine Biology</i> 159: 2731–2742. </p><p>La Peyre MK, Aguilar Marshall D, Miller LS, Humphries AT (2019) Oyster Reefs in Northern Gulf of Mexico Estuaries Harbor Diverse Fish and Decapod Crustacean Assemblages: A Meta-Synthesis.<br><i>Frontiers in Marine Science</i>. 6:666. doi: 10.3389/fmars.2019.0066</p><p>Miller PJ (1979) Adaptiveness and implications of small size in Teleosts. <i>Symposia of the Zoological Society of London.</i> 44: 263–306</p><p>Møller PR, Knudsen W, Schwarzhans W, Nielsen JG (2016) A new classification of viviparous brotulas (Bythitidae) – with family status for Dinematichthyidae – based on molecular, morphological and fossil data. <i>Molecular Phylogenetics and Evolution</i> 100: 391-408. <a href="https://doi.org/10.1016/j.ympev.2016.04.008">https://doi.org/10.1016/j.ympev.2016.04.008</a></p><p>Pinheiro H, Goodbody-Gringley G, Jessup M, Shepherd B, Chequer A, Rocha L (2016) Upper and lower mesophotic coral reef fish communities evaluated by underwater visual censuses in two Caribbean locations. <i>Coral Reefs</i> 35: 139–151 DOI 10.1007/s00338-015-1381-0</p><p>Robertson DR, Smith-Vaniz WF (2008) Rotenone: An essential but demonized tool for assessing marine fish diversity. <i>Bioscience </i>58:165-170.</p><p>Robertson DR, Smith-Vaniz WF (2010) Use of clove oil in collecting coral reef fishes for research.<i> Marine Ecology Progress Series.</i>401:295-302</p><p>Smith-Vaniz WF, Jelks HL, Rocha LA (2006) Relevance of cryptic fishes in biodiversity assessments: A case study at Buck Island National Monument, St. Croix. <i>Bulletin of Marine Science </i>79:17–48</p><p>Stefanoudis PV, Gress E, Pitt JM, Smith SR, Kincaid T, Rivers M, Andradi-Brown DA, Rowlands G, Woodall LC and Rogers AD (2019) Depth-Dependent Structuring of Reef Fish Assemblages From the Shallows to the Rariphotic Zone. <i>Frontiers in Marine Science</i>. 6:307 doi: 10.3389/fmars.2019.00307</p><p>Willis TJ (2001). Visual census methods underestimate density and diversity of cryptic reef fishes. <i>Journal of Fish Biology</i> 59: 1408-1411.</p>
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