Reef-associated Bony Fishes of the Tropical Eastern Pacific: 2024 (VERSION 1) DATABASE

Reef-associated Bony Fishes of the Tropical Eastern Pacific: 2024 (VERSION 1) DATABASE

 Date: September 30, 2024;        DOI 10.5281/zenodo.13863109

 https://zenodo.org/records/13863109

Introduction to the First Version

This first version of the database includes bony fishes belonging to families present in the Tropical Eastern Pacific (TEP) biogeographic region that associate with coral and rocky reefs. That region extends from Magdalena Bay on the southwest coast of Baja California, through the Gulf of California and south to about Cabo Blanco, northern Peru, and includes five isolated oceanic islands and island groups: Clipperton, Cocos, the Galapagos archipelago, Malpelo and the Revillagigedo archipelago.

The objective here is to provide a database of the entire regional fauna of reef-associated bony fishes that includes information on its taxonomic composition and a range of biological and biogeographic characteristics of listed species. This is intended to facilitate comparisons of the structure of equivalent regional faunas in different biogeographic regions, and for examining local variation in faunal structure within the TEP.

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). A database for reef-associated bony fishes in Greater Caribbean (Robertson & Tornabene, 2023) focuses on species belonging to those families, because those are what are traditionally considered to be Reef Fishes. This database takes the same approach.

The list includes not only TEP endemics and other eastern Pacific species that also occur to the north and south of the TEP but also transpacific species (Robertson et. al. 2004) that dispersed across the 4000 km wide East Pacific Barrier and have resident populations in the TEP. It does not include non-native species introduced for aquaculture purposes (e.g. Rachycentron canadum, Sparus aurata) or that have passed through the Panama Canal from the Caribbean and occur in the TEP (e.g. Megalops atlanticus). Species other than regional endemics, which dominate the fauna, are considered to be residents in the TEP if there are numerous records of them in the region, particularly records in different years and at different locations. 

Members of a few families of bony fishes that are found only on deep-water reefs (i.e. often below the 150 m lower limit of the mesophotic zone) and have no representatives associated with shallow reefs in the TEP, are not included among the Reef Fish families. Between them those families have only a few (13) reef-associated species resident in the TEP that live on deep reefs. Another 60 species (28 of them Transpacifics; see below) of reef-associated fishes that do not appear to have resident populations in the TEP also are not included in the current list.

Reef-associated fishes include not only demersal and benthic species that use consolidated hard substrata found on both coral- and rocky reefs, but also demersal and benthic species that use soft bottoms (sand, gravel, mud, seagrass and macroalgal beds growing on sediment, estuaries and mangroves) immediately adjacent to or within the matrices of reefs.  Benthic species are restricted to living on and in the benthic habitats, whereas Demersal species use and rely on both the bottom and the near-bottom water column. These two categories both relate to the behavior of fishes during the day, which, in some cases, changes at night. The Flashlight Fish Phthanophaneron harveyi is not included because it apparently hides in deeper water reefs during the day and enters shallow water only at night. Apogonids and Holocentrids are benthic during the day, but demersal when they become active at night, and day-active demersal species often become cryptobenthic at night by hiding within reef substrata (e. g. some wrasses rest in reef structures, while others bury themselves in sand). Reef-associated fishes also include Pelagic species that live in the water column and facultatively associate with reefs, are regularly seen over and immediately adjacent to them, and have trophic interactions with organisms on reefs. They do so either by contributing food to reefs (e.g. parasites removed from pelagic fishes such as Mola alexandrini in the Galapagos by reef fishes; see images of that activity in iNaturalist) or by extracting food from them, e.g. by preying on reef fishes. For example, Yellowfin Tuna, Thunnus albacares (and Silky Shark, Carcharhinus falciformis) prey on Cephalopholis colonus at Cocos Island; see Auster et al. 2019). Usage of the term reef-associated here  is similar to the definition used by FishBase (https://fishbase.mnhn.fr/glossary/glossary.php ) in that it includes fishes living near as well as on reefs, but more expansive than FishBase’s restriction of the term to coral reefs.

Species found almost exclusively in fresh- to brackish water also are excluded from the list. Finally, excluded species include a few taxa of oceanic pelagic fishes that are found in surface waters that may be seen in the general vicinity reefs: Exocoetidae, Xiphiidae, Istiophoridae and some of the large (Thunnus) tunas. 

Cryptobenthic fishes 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 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 have been classed as cryptobenthic. While individuals of some cryptobenthic species, such as Muraenids and Apogonids may regularly be seen during the day on reefs, it is not possible to know what fraction of their populations the invisible individuals represent (Willis 2001; Alzate et al 2014). On the other hand, some species belonging to families that contain many cryptobenthic species but, because they school in the water just above the substratum are actually demersal, and the Garden Eels (Heteroconger spp.) that extend their long, slender bodies to feed in the water column above their burrows are not classed as cryptobenthic here because they can be reliably censused visually.

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 which cryptobenthic reef-fishes are small, 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 12 of which are in the TEP) that have relatively large numbers of small, cryptobenthic species, share many life-history characteristics and are important for energy flow in reef ecosystems as Core families of Cryptobenthic Reef-fishes (Core CRFs). Members of those families (Apogonidae, Blenniidae, Bythitidae, Callionymidae, Chaenopsidae, Dactyloscopidae, Gobiidae, Gobiesocidae, Labrisomidae, Opistognathidae, Syngnathidae, Tripterygiidae), which Brandl et al. (2018, 2019) also referred to as microbenthic reef fishes, are identified in the list. Shortly before Brandl et al (2018) defined the group of Core CRFs, the Bythitidae was split into two families, Bythitidae and Dinematichthyidae. Both those families are included here 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 Serranidae).

Shallow- and deep-reef fishes: Shallow-water species are those with populations restricted to or concentrated at depths above 40m. Deep-reef species have populations concentrated in or restricted to depths greater than 40m. This depth boundary 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.  Shallow species also include those that may have shallow populations at some sites in the TEP, but only deep populations elsewhere and species in which juveniles are common in shallow water and adults are restricted to deep water.

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. I 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.

Other types of data in the database:

The database also contains information on the maximum and minimum depths of the Depth Range,  maximum Total Length (TL), whether each species is a TEP endemic (with at least 90% of its range in the TEP); whether a species is a Transpacific Immigrant from the central pacific that recruited across the Eastern Pacific Barrier, whether it has a Small Geographic Range (up to 1/3 of the TEP) whether it has a Very Small Geographic range (not more than 10% of the TEP) and whether it is restricted to one or more of the Oceanic Islands in the TEP.

Redlist Extinction Risk category. Since the early 2000s the IUCN Red List (https://www.iucnredlist.org/) has produced a comprehensive set of assessments of TEP fishes. Those include assessments for >90% of the species in the present database. Those assessment documents include much information on habitat usage by those fishes that was relevant to the construction of the present database.  Assigned Redlist categories of extinction risk used here are NE (Not Evaluated), DD (Data Deficient), LC (Least Concern), VU (Vulnerable), NT (Near Threatened), EN (Endangered) and CR (Critically Endangered).

                Sources of data: 

Besides the publications listed in the bibliography, the species list is based on personal observations and research Panama, Costa Rica, El Salvador, Mexico, the Revillagigedo and Galapagos archipelagos, Clipperton, Cocos and Malpelo Islands. Much of those data and data based on a large range of other sources is available in the website Shorefishes of the Tropical Eastern Pacific: an information system (www.stri.org/sftep). The species list also draws on reviews of photographs in the website www.iNaturalist.org and recent live-fish photographs taken by citizen-scientist underwater photographers (principally Carlos and Allison Estape; see https://carlosestape.photoshelter.com/gallery-list) at the Midriff Islands in the Gulf of California, southern Baja, the Revillagigedo, Cocos and Galapagos Islands and nearshore islands (Coiba area and the Pearl Islands) of Panama.

The reef-associated bony-fish fauna of the TEP

This first edition of the database includes 739 species belonging to 310 genera and 87 families. Of those 254 (34.4%) are demersal species, 400 (54.1%) are benthic species and 85 (11.5%) are pelagic species. Among them are 222 small (<10cm TL) cryptobenthic forms (30.0% of the fauna) and 261 Core-CRF species (35.3% of the fauna).  Further, only 58 species (7.8% of the total) are deep-reef forms, with 23 of that group demersal (9.1% of all demersal forms), 35 benthic (8.8% of all benthic species), 7 small cryptobenthic types (3.2% of that entire group) and 8 Core-CRF species (3.1% of that entire group).

The classification of families and spelling of scientific names generally follows Eschmeyer’s Catalog of Fishes. (https://www.calacademy.org/scientists/projects/eschmeyers-catalog-of-fishes

Hosting of this database by Zenodo will allow it to be updated through the production of new versions as new information becomes available.

New information, comments or queries relating to the classification or species list should be directed to [e-mail].

Bibliography of publications and databases relating to the construction of this list:

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