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Species ecology explains the various spatial components of genetic diversity in tropical reef fishes
<p>Generating genomic data for 19 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diver- sity patterns from local to regional scales. We distinguish between the α, β and γ components of genetic diversity, which we subsequently link to six ecological traits. We find that the α and γ components of genetic diversity are strongly correlated so that species with a high total regional genetic diversity display systematically high local diversity. The α and γ diversity components are negatively associated with species abundance recorded using underwater visual surveys and positively with body size. Pelagic larval duration is found to be negatively related to genetic β diversity supporting its role as a dispersal trait in marine fishes. Deviation from the neutral theory of molecular evolution motivates further effort to understand the processes shaping genetic diversity and ultimately the diversification of the exceptional diversity of tropical reef fishes.</p>
The Reef Fish faunas of 6 sites in the Greater Caribbean: Alligator Reef, Bermuda, Curacao, Roatan, St. Croix and St. Eustatius
<p>Species of marine fishes in Families with members known to associate with shallow reefs in the Greater Caribbean. For each species its island(s) of occurrence are indicated, together with whether or not it is a reef-associate, its habitat usage (pelagic, demersal or benthic), for benthic species whether or not it is cryptobenthic, whether or not it is a member of a Core Coral Reef Fish Family, whether or not is maximum size is less than 10 cm TL, and whether or not it is restricted to deep water , ie below 40 m. </p> <p>These ecological characteristics are described in more detail in: Robertson DR, Tornabene L (2020) Reef-associated Bony Fishes of the Greater Caribbean: A Checklist (VERSION 3). <a href="https://zenodo.org/record/3974538#.X7a0W81KiUl">Zenodo</a>. DOI 10.5281/zenodo.4279301 </p>
Reef-associated Bony Fishes of the Greater Caribbean: a Checklist; Version 4
<p><strong> Reef-associated Bony Fishes of the Greater Caribbean: A Checklist (VERSION 4)</strong></p> <p> </p> <p> Date: October 22, 2021. DOI 10.5281/zenodo.5592149</p> <p> </p> <p><strong>D Ross Robertson</strong> </p> <p>Smithsonian Tropical Research Institute, Balboa, Republic of Panama. Robertsondr@si.edu</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. Luke.Tornabene@gmail.com</p> <p> </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. Information used here was extracted from 185 publications about Greater Caribbean reef fishes and 152 publications on Brazilian reef 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 83 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, Symphysanodontidae, Trachichthyidae, and Triacanthodidae. Between them those 14 families have a total of ~41 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 non-native species with resident populations in the Greater Caribbean, notably <em>Pterois volitans</em> and <em>Neopomacentrus cyanomos</em>.</p> <p><strong><em>Reef-associated fishes</em></strong> include 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 <em>Thalassoma bifasciatum</em> rest inside tubular sponges, while <em>Halichoeres bivittatus</em> 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.</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 (<em>Thunnus)</em> tunas. </p> <p><strong><em>Cryptobenthic fishes</em></strong> 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 (<em>Coryphopterus hyalinus </em>and<em> C. personatus</em>) that school in the water just above the substratum, and the Garden Eels (<em>Heteroconger spp.</em>) 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><strong><em>Shallow- and deep-reef fishes</em></strong>: 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). We classified as shallow some species that have shallow populations at some sites in the Greater Caribbean and deep populations in others (e. g. <em>Gramma melacara</em>), and others in which juveniles are common in shallow water and adults are restricted to deep water (e. g. <em>Lutjanus buccanella</em>).</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> </p> <p> </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>83 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> </p> <p> </p> <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<em>). </em></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 <em>Lipogramma</em>), Labrids (2 species of <em>Decodon</em>) and Serranids (1 species of <em>Baldwinella</em>) 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 <em>Marine Ecology Progress Series</em> 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. <em>Revista Biologica Tropical </em>62 (Supplement 1): 359–371.</p> <p>Baldwin CC, Tornabene L, Robertson DR (2018) Below the mesophotic. <em>Scientific Reports</em> 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. <em>Journal of the Marine Biological Association of the U.K. 86: 1221-1228.</em></p> <p>Brandl SJ, Goatley CHR, Bellwood DR, Tornabene L (2018) The hidden half: ecology and evolution of cryptobenthic fishes on coral reefs. <em>Biological reviews of the Cambridge Philosophical Society 93:</em> 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 V, Schiettekatte MD, Bellwood DR (2019) Demographic dynamics of the smallest marine vertebrates fuel coral reef ecosystem functioning<em>. Science</em> 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. <em>Marine Ecology Progress Series</em> 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. <em>Frontiers in Marine Science</em> 5:303. doi:10.3389/fmars.2018.00303</p> <p>Gilmore, RG Jr (2016) You can’t catch a fish with a robot. <em>Gulf and Caribbean Research</em> 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. <em>Journal of Shellfish Research</em> 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. <em>Marine Biology</em> 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> <em>Frontiers in Marine Science</em>. 6:666. doi: 10.3389/fmars.2019.0066</p> <p>Miller PJ (1979) Adaptiveness and implications of small size in Teleosts. <em>Symposia of the Zoological Society of London.</em> 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. <em>Molecular Phylogenetics and Evolution</em> 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. <em>Coral Reefs</em> 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. <em>Bioscience </em>58:165-170.</p> <p>Robertson DR, Smith-Vaniz WF (2010) Use of clove oil in collecting coral reef fishes for research.<em> Marine Ecology Progress Series.</em>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. <em>Bulletin of Marine Science </em>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. <em>Frontiers in Marine Science</em>. 6:307 doi: 10.3389/fmars.2019.00307</p> <p>Willis TJ (2001). Visual census methods underestimate density and diversity of cryptic reef fishes. <em>Journal of Fish Biology</em> 59: 1408-1411.</p> <p><strong> Reef-associated Bony Fishes of the Greater Caribbean: A Checklist (VERSION 4)</strong></p> <p> </p> <p> Date: October 22, 2021</p> <p> </p> <p><strong>D Ross Robertson</strong> </p> <p>Smithsonian Tropical Research Institute, Balboa, Republic of Panama. Robertsondr@si.edu</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. Luke.Tornabene@gmail.com</p> <p> </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. Information used here was extracted from 185 publications about Greater Caribbean reef fishes and 152 publications on Brazilian reef 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 83 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, Symphysanodontidae, Trachichthyidae, and Triacanthodidae. Between them those 14 families have a total of ~41 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 non-native species with resident populations in the Greater Caribbean, notably <em>Pterois volitans</em> and <em>Neopomacentrus cyanomos</em>.</p> <p><strong><em>Reef-associated fishes</em></strong> include 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 <em>Thalassoma bifasciatum</em> rest inside tubular sponges, while <em>Halichoeres bivittatus</em> 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.</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 (<em>Thunnus)</em> tunas. </p> <p><strong><em>Cryptobenthic fishes</em></strong> 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 (<em>Coryphopterus hyalinus </em>and<em> C. personatus</em>) that school in the water just above the substratum, and the Garden Eels (<em>Heteroconger spp.</em>) 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><strong><em>Shallow- and deep-reef fishes</em></strong>: 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). We classified as shallow some species that have shallow populations at some sites in the Greater Caribbean and deep populations in others (e. g. <em>Gramma melacara</em>), and others in which juveniles are common in shallow water and adults are restricted to deep water (e. g. <em>Lutjanus buccanella</em>).</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>83 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><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<em>). </em></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> <ol> <li>A few, currently unnamed species of reef-associated Gobiids (6 species in two, currently unnamed, genera), Grammatids (2 species of <em>Lipogramma</em>), Labrids (2 species of <em>Decodon</em>) and Serranids (1 species of <em>Baldwinella</em>) for which sufficient ecological information is available have been added to the list.</li> <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> <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> <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 <em>Marine Ecology Progress Series</em> 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. <em>Revista Biologica Tropical </em>62 (Supplement 1): 359–371.</p> <p>Baldwin CC, Tornabene L, Robertson DR (2018) Below the mesophotic. <em>Scientific Reports</em> 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. <em>Journal of the Marine Biological Association of the U.K. 86: 1221-1228.</em></p> <p>Brandl SJ, Goatley CHR, Bellwood DR, Tornabene L (2018) The hidden half: ecology and evolution of cryptobenthic fishes on coral reefs. <em>Biological reviews of the Cambridge Philosophical Society 93:</em> 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 V, Schiettekatte MD, Bellwood DR (2019) Demographic dynamics of the smallest marine vertebrates fuel coral reef ecosystem functioning<em>. Science</em> 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. <em>Marine Ecology Progress Series</em> 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. <em>Frontiers in Marine Science</em> 5:303. doi:10.3389/fmars.2018.00303</p> <p>Gilmore, RG Jr (2016) You can’t catch a fish with a robot. <em>Gulf and Caribbean Research</em> 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. <em>Journal of Shellfish Research</em> 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. <em>Marine Biology</em> 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> <em>Frontiers in Marine Science</em>. 6:666. doi: 10.3389/fmars.2019.0066</p> <p>Miller PJ (1979) Adaptiveness and implications of small size in Teleosts. <em>Symposia of the Zoological Society of London.</em> 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. <em>Molecular Phylogenetics and Evolution</em> 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. <em>Coral Reefs</em> 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. <em>Bioscience </em>58:165-170.</p> <p>Robertson DR, Smith-Vaniz WF (2010) Use of clove oil in collecting coral reef fishes for research.<em> Marine Ecology Progress Series.</em>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. <em>Bulletin of Marine Science </em>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. <em>Frontiers in Marine Science</em>. 6:307 doi: 10.3389/fmars.2019.00307</p> <p>Willis TJ (2001). Visual census methods underestimate density and diversity of cryptic reef fishes. <em>Journal of Fish Biology</em> 59: 1408-1411.</p>
Data from "Behavior of reef fishes during a submarine magnitude 5 earthquake"
<p><strong>Behavior of reef fishes during a submarine magnitude 5 earthquake</strong></p> <p>Appendix S1 gathers video excerpts of 2 minutes recorded by 12 remote underwater cameras on the seafloor of N’Gouja reef (Mayotte) before, during and after the magnitude 5.3 earthquake on 10 November 2020 (12:19:39 local time).</p> <p>Table S1 & Tables S2 gathers data of fish behavior collected from the 12 remote underwater videos (rows) during 10 seconds slots before [be.], during [Earthq.] and after [af.] the earthquake (columns). Table S1 contains the proportion of fish individuals seen fleeing. Table S2 contains the feeding activity of <em>Ctenochaetus striatus</em> (number of bites per individual during 10 s).</p>
Multi-decadal stability of fish productivity despite increasing coral reef degradation
<p>1. Under current trajectories, it is unlikely that the coral reefs of the future will resemble those of the past. As multiple stressors, such as climate change and coastal development, continue to impact coral reefs, understanding the changes in ecosystem functioning is imperative to protect key ecosystem services.</p> <p>2. We used a 26-year dataset of benthic reef fishes (including cryptobenthic fishes) to identify multi-decadal trends in fish biomass production on a degraded coral reef. We converted fish abundances into estimates of community productivity to track the long-term trend of fish biomass production through time.</p> <p>3. Following the first mass coral bleaching event in 1998, the abundance, standing biomass, and productivity of fish communities remained remarkably constant through time, despite the occurrence of multiple stressors, including extreme sedimentation, cyclones, and mass coral bleaching events. Species richness declined following the 1998 bleaching event, but rebounded to pre-bleaching levels and also remained relatively stable.</p> <p>4. Although the species composition of the communities changed over time, these new community configurations still maintain a steady level of fish biomass production. While these highly dynamic and increasingly degraded systems can still provide some critical ecosystem functions, it is unclear whether these patterns will remain stable over future decades.</p>
Data from: The role of fish feces for nutrient cycling on coral reefs
<p>Consumers play an important role in biogeochemical cycles through the consumption and release of essential elements such as carbon (C), nitrogen (N), and phosphorus (P). Indeed, a large proportion of consumed elements are released into the environment in inorganic (i.e., excretion) or organic form (i.e., egestion). On coral reefs, fishes represent the bulk of consumer biomass and thus play a key role in the recycling of nutrients. In recent years, excretion rates have been studied intensively, but less is known about the rate and quality of coral reef fish egestion. In this study, we quantify the elemental contents of fish feces, estimate absorption efficiencies and compare egestion and excretion rates for 51 coral reef fish species. We show that elemental concentrations decrease remarkably little from food to feces. This is due to extremely low absorption efficiencies, resulting in the egestion of large amounts of energy and nutrients. Moreover, we show that while the quality of fish feces varies across trophic guilds, it remains highly variable within trophic guilds. Finally, we demonstrate that the release of N and P through egestion outweighs the amount of nutrients recycled through excretion. Our study highlights the need to incorporate animal egestion into assessments of ecosystem functioning and food web structure.</p>
Documenting Reef-Fish Diversity in the Revillagigedo Archipelago, Pacific Mexico, November 2022
<p>Documenting Reef-Fish Diversity in the Revillagigedo Archipelago, Pacific Mexico, November 2022</p> <p>By Allison Morgan Estape, Citizen Scientist</p> <p>150 Nautilus Drive Islamorada, Florida 33036, USA. Email: <a href="mailto:allison.carlos@me.com">allison.carlos@me.com</a>. </p> <p>Photographic Website: <a href="https://carlosestape.photoshelter.com/gallery-list">https://carlosestape.photoshelter.com/gallery-list</a>.</p> <p>Between November 20 and December 2, 2022, a group of seven professional ichthyologists from Mexico, Panama and the USA, together with 11 SCUBA-diving photographers experienced in taking diagnostic images of reef-fishes, conducted a scientific expedition aboard the diving-support vessel Quino El Guardian to the Revillagigedo Archipelago, a Mexican Marine Protected Area that lies 250 miles south-southwest of the tip of Baja California. The objectives of the expedition were (1) to photograph all observed species of reef-fishes in their natural habitat at each of the archipelago’s four islands to provide permanent documentation of such species occurrences; and (2) to collect specimens for museums in Mexico and the United States at which they would be used for morphological and genetic assessments of endemism in the archipelagos’ reef-fish fauna and the general relationships of that fauna to the reef-fish fauna of Mexico and other parts of the Tropical Eastern Pacific. This video of a power-point show provides a visual record of the expedition and summarizes the results by island and the expedition’s overall findings to date.</p>
Environmental DNA highlights the influence of salinity and agricultural run-off on coastal fish assemblages in the Great Barrier Reef region
<p class="MsoNormal">Agricultural run-off in Australia's Mackay-Whitsunday region is a major source of nutrient and pesticide pollution to the coastal and inshore ecosystems of the Great Barrier Reef. While the effects of run-off are well documented for the region's coral and seagrass habitats, the ecological impacts on estuaries, the direct recipients of run-off, are less known. This is particularly true for fish communities, which are shaped by the physico-chemical properties of the coastal waterways that vary greatly in tropical regions. To address this knowledge gap, we used environmental DNA (eDNA) metabarcoding to examine teleost and elasmobranch fish assemblages at four locations (three estuaries and a harbour) subjected to varying levels of agricultural run-off during a wet and dry season. Pesticide and nutrient concentrations were markedly lower during the sampled dry season. With the influx of freshwater and agricultural run-off during the wet season, teleost and elasmobranch taxa richness significantly decreased in all three estuaries, along with pronounced changes in fish community composition which were largely associated with environmental variables (particularly salinity). In contrast, the nearby Mackay Harbour exhibited a far more stable community structure, with no marked changes in fish assemblages observed between the sampled seasons. Within the wet season, differing compositions of fish communities were observed among the four sampled locations, with this variation being significantly correlated with environmental variables (salinity, chlorophyll, DOC) and contaminants from agricultural run-off, i.e., nutrients (nitrogen and phosphorus) and pesticides. Historically contaminated and relatively unimpacted estuaries each demonstrated distinct fish communities, reflecting their associated catchment use. Our findings emphasise that while seasonal effects (e.g., changes in salinity) play a key role in shaping the community structure of estuarine fish in this region, agricultural contaminants (nutrients and pesticides) are also important contributors in some systems.</p>
Figure 10. - Different fish abundance dynamic profiles between 1983 and 2014 in Long term monitoring of coral and fish assemblages (1983-2014) in Tiahura reefs, Moorea, French Polynesia
Figure 10. - Different fish abundance dynamic profiles between 1983 and 2014 on the outer slope at Tiahura sector in Moorea.
Figure 6 in Long term monitoring of coral and fish assemblages (1983-2014) in Tiahura reefs, Moorea, French Polynesia
Figure 6. - Commercial fish abundance at Tiahura sector in Moorea for the barrier reef and outer slope. Second-degree polynomial models were fitted to data (*: 0.01 <p ≤ 0.05, **: 0.001 <p≤ 0.01).
Figure 4 in Long term monitoring of coral and fish assemblages (1983-2014) in Tiahura reefs, Moorea, French Polynesia
Figure 4. - Total fish abundance at Tiahura sector in Moorea for the fringing reef. Second degree polynomial models were fitted to data (*: 0.01 <p ≤ 0.05, **: 0.001 <p ≤ 0.01).
Figure 9 in Long term monitoring of coral and fish assemblages (1983-2014) in Tiahura reefs, Moorea, French Polynesia
Figure 9. - Herbivorous fish species richness at Tiahura sector in Moorea for the three habitats. Linear models were fitted to data (**: 0.001 <p ≤ 0.01; ***: p ≤ 0.001).
Figure 5 in Long term monitoring of coral and fish assemblages (1983-2014) in Tiahura reefs, Moorea, French Polynesia
Figure 5. - Total fish species richness at Tiahura sector in Moorea for the fringing reef. Linear models were fitted to data (***: p ≤ 0.001).
Figure 8 in Long term monitoring of coral and fish assemblages (1983-2014) in Tiahura reefs, Moorea, French Polynesia
Figure 8. - Herbivorous fish abundance at Tiahura sector in Moorea for the barrier reef and outer slope. Linear models were fitted to data (**: 0.001 <p ≤ 0.01).
Figure 3 in Long term monitoring of coral and fish assemblages (1983-2014) in Tiahura reefs, Moorea, French Polynesia
Figure 3. - Temporal dynamics in coral percentage cover on the outer slope of Tiahura sector from 1979 to 2011. Stars denote the five main disturbances that affected the reef over the study period (COTS: Acanthaster planci outbreak). Dotted lines correspond to linear interpolation of coral percentage cover.
Colour dimorphism in labrid fishes as an adaptation to life on coral reefs
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Data from: Body shape and mode of propulsion do not constrain routine swimming in coral reef fishes
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Data for: Fish feces reveal diverse nutrient sources for coral reefs
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Data from: Functional diversity shapes the stability of reef fish biomass under global change
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Context-dependent multimodal behaviour in a coral reef fish: Stage 1 & 2 total duration and count data in behaviour trials
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