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Species ecology explains the various spatial components of genetic diversity in tropical reef fishes
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Data from: Accelerated diversification explains the exceptional species richness of tropical characoid fishes
<p>The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1288 ultraconserved element loci spanning 293 species, 211 genera, and 21 families of characoid fishes to reconstruct a new, fossil-calibrated phylogeny and infer the most likely diversification scenario for a clade that includes a third of Neotropical fish diversity. This phylogeny implies paraphyly of the traditional delimitation of Characiformes because it resolves the largely Neotropical Characoidei as the sister lineage of Siluriformes (catfishes), rather than the African Citharinodei. Time-calibrated phylogenies indicate an ancient origin of major characoid lineages and reveal a much more recent emergence of most characoid species. Diversification rate analyses infer increased speciation and decreased extinction rates during the Oligocene at around 30 Ma during a period of mega-wetland formation in the proto-Orinoco-Amazonas. Three species rich and ecomorphologically diverse lineages (Anostomidae, Serrasalmidae, and Characidae) that originated more than 60 Ma in the Paleocene experienced particularly notable bursts of Oligocene diversification and now account collectively for 68% of the approximately 2150 species of Characoidei. In addition to paleogeographic changes, we discuss potential accelerants of diversification in these three lineages. While the Neotropics accumulated a museum of ecomorphologically diverse characoid lineages long ago, this geologically dynamic region also cradled a much more recent birth of remarkable species-level diversity.</p>
Fig. 3 in Fish functional groups in a tropical wetland of the Yucatan Peninsula, Mexico
Fig. 3. Relative biomass abundance of functional groups among habitats and seasons.
Fig. 1 in Fish functional groups in a tropical wetland of the Yucatan Peninsula, Mexico
Fig. 1. Geographic location of the study site (white star) in Sian Ka'an Biosphere Reserve, Mexico.
Critical thermal maxima of early life stages of tropical fishes
<p>Marine ectotherms are often sensitive to thermal stress, and certain life stages can be particularly vulnerable (e.g., larvae or spawners). In this study, we investigated the critical thermal maxima (CT<sub>max</sub>) of larval and early juvenile life stages of three tropical marine fishes (<i>Acanthochromis polyacanthus</i>, <i>Amphiprion melanopus,</i> and <i>Lates calcarifer</i>). We tested for potential effects of developmental acclimation, life stage, and experimental heating rates, and we measured metabolic enzyme activities from aerobic (citrate synthase, CS) and anaerobic pathways (lactate dehydrogenase, LDH). A slightly elevated rearing temperature neither influenced CT<sub>max</sub> nor CS activity, which otherwise could have indicated thermal acclimation. However, we found species- and life stage-specific differences in CT<sub>max</sub> that were mainly explained by body mass, with faster heating rates leading to higher CT<sub>max</sub>. Acute temperature stress did not change CS or LDH activities, suggesting that overall aerobic and anaerobic metabolism remained stable. <i>Lates calcarifer</i>, a catadromic species that migrates from oceanic to riverine habitats upon metamorphosis, had higher CT<sub>max</sub> than the two coral reef fish species. We highlight that, for obtaining conservative estimates of a fish species' upper thermal limit, several developmental stages and body mass ranges should be examined. Moreover, upper thermal limits should be assessed using standardized heating rates. This will not only benefit comparative approaches but also aid in assessing geographic (re-) distributions and climate change sensitivity of marine fishes.</p>
Variation in functional composition of reef fishes along a tropical to temperate gradient
<p><strong>Aims</strong><br>Transformations of species and functional compositions on subtropical reefs are ongoing due to poleward range shifts of some tropical species, with largely unknown consequences to ecosystem functioning. Trait-based approaches are powerful tools to quantify such changes. Here, we evaluated changes in the trait composition of coral-associated fish communities along a tropical to a temperate environmental gradient of ca.1400 km in southern Japan with abundance-weighted trait expression to assess how trait complexity changes with increasing latitude.</p> <p><strong>Location</strong><br>Ryukyu Islands and southern Pacific coast of Japan</p> <p><strong>Taxon</strong><br>Reef fish</p> <p><strong>Methods</strong><br>We tested for shifts in trait space and functional redundancy, based on five morphological, life history, and behavioural traits: maximum length, pelagic larval duration, trophic level, substrate preference, and reproductive mode. Our trait database was coded with two approaches, first, by attributing a single value to each trait per species, and second, by fuzzy coding that allows more than one value per trait and hence considers some intraspecific trait variation.</p> <p><strong>Results</strong><br>We found a reduction in specialist habitat traits (coral substrate preference, nesters, herbivores) and an increase in generalist traits (predators) with increasing latitude, along with a contraction in trait space from tropical to temperate reefs. Functional redundancy declined with increasing latitude. These trends were closely linked with latitudinal gradients in temperature, along with changes in other environmental factors such as turbidity and photosynthetically active radiation.</p> <p><strong>Main Conclusion</strong><br>Functional turnover and contractions are thus likely due to the marginal conditions for coral-associated fishes at higher latitudes, favouring generalist species, whereas increased resources at lower latitudes favour high redundancy and niche partitioning. Accounting for intraspecific trait variation indicated the same trends but highlighted increased functional vulnerability across all sites. We show that trait complexity in coral-associated fish communities decreases from tropical to temperate reefs, highlighting the reduced functional scope that comes with marginal environmental conditions.</p>
Fig. 2 in Dynamics of fish assemblages on a continuous rocky reef and adjacent unconsolidated habitats at Fernando de Noronha Archipelago, tropical western Atlantic
Fig. 2. Mean values (±SE) of temporal fluctuation and temporal stability.
Fig. 3 in Habitat preferences of common native fishes in a tropical river in Southeastern Brazil
Fig. 3. Depth preferences of seven dominant native fish species in the Guandu River.
Fig. 4 in Habitat preferences of common native fishes in a tropical river in Southeastern Brazil
Fig. 4. Velocity preferences of seven dominant native fish species in the Guandu River.
Fig. 1 in Total mercury in the fish Trichiurus lepturus from a tropical estuary in relation to length, weight, and season
Fig. 1. Location and details of the study area, Goiana Estuary at the Brazilian Northeast.
Reef-associated Bony Fishes of the Tropical Eastern Pacific: 2024 (VERSION 1) DATABASE
<p><strong> <u>Reef-associated Bony Fishes of the Tropical Eastern Pacific: 2024 (VERSION 1) DATABASE </u></strong></p> <p> Date: September 30, 2024; <strong>DOI </strong><strong>10.5281/zenodo.13863109</strong></p> <p><strong> https://zenodo.org/records/13863109</strong></p> <p><u>I<strong>ntroduction to the First Version</strong></u></p> <p>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.</p> <p>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.</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). 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 <strong>Reef Fishes</strong>. This database takes the same approach.</p> <p>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. <em>Rachycentron canadum, Sparus aurata</em>) or that have passed through the Panama Canal from the Caribbean and occur in the TEP (e.g. <em>Megalops atlanticus</em>). Species other than regional endemics, which dominate the fauna, are considered to be <strong>residents</strong> in the TEP if there are numerous records of them in the region, particularly records in different years and at different locations. </p> <p>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.</p> <p><strong><em>Reef-associated fishes</em></strong> include not only <strong>demersal and benthic species that use consolidated hard substrata</strong> found on both 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 benthic habitats, 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. The Flashlight Fish <a name="_Hlk178058223"></a><em>Phthanophaneron harveyi</em> 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 <strong>Pelagic species</strong> that live in the water column and facultatively associate with reefs, are regularly seen over and immediately adjacent to them, and <strong>have trophic interactions with organisms on reefs. </strong>They do so<strong> </strong>either by contributing food to reefs (e.g. parasites removed from pelagic fishes such as <em>Mola alexandrini</em> 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, <em>Thunnus albacares</em> (and Silky Shark, <em>Carcharhinus falciformis</em>) prey on <em>Cephalopholis colonus</em> at Cocos Island; see Auster et al. 2019). Usage of the term reef-associated here is similar to the definition used by FishBase (<a href="https://fishbase.mnhn.fr/glossary/glossary.php">https://fishbase.mnhn.fr/glossary/glossary.php</a> ) 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.</p> <p>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 (<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 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 (<em>Heteroconger spp.</em>) 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.</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><strong>,</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 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 <strong>Core families of Cryptobenthic Reef-fishes (Core CRFs)</strong>. 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 <strong>microbenthic reef fishes</strong><strong>,</strong> 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).</p> <p><strong><em>Shallow- and deep-reef fishes</em></strong>: 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. <strong> </strong>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.</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. 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.</p> <p><strong><u>Other types of data in the database:</u></strong></p> <p>The database also contains information on the maximum and minimum depths of the <strong>Depth Range,</strong> maximum <strong>Total Length</strong> (TL), whether each species is a <strong>TEP endemic</strong> (with at least 90% of its range in the TEP); whether a species is a <strong>Transpacific Immigrant</strong> from the central pacific that recruited across the Eastern Pacific Barrier, whether it has a <strong>Small Geographic Range</strong> (up to 1/3 of the TEP) whether it has a <strong>Very Small Geographic range</strong> (not more than 10% of the TEP) and whether it is restricted to one or more of the <strong>Oceanic Islands</strong> in the TEP.</p> <p><strong>Redlist Extinction Risk category. </strong>Since the early 2000s 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 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).</p> <p><strong> <u>Sources of data:</u></strong> </p> <p>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<strong><em> Shorefishes of the Tropical Eastern Pacific: an information system</em></strong> (<a href="http://www.stri.org/sftep">www.stri.org/sftep</a>). The species list also draws on reviews of photographs in the website <a href="http://www.iNaturalist.org">www.iNaturalist.org</a> and recent live-fish photographs taken by citizen-scientist underwater photographers (principally Carlos and Allison Estape; see <a href="https://carlosestape.photoshelter.com/gallery-list">https://carlosestape.photoshelter.com/gallery-list</a>) 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.</p> <p><strong><u>The reef-associated bony-fish fauna of the TEP</u></strong><strong> </strong></p> <p><strong>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).</strong></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>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> </p> <p><strong>Bibliography of publications and databases relating to the construction of this list:</strong></p> <p>1. Aburto-Oropeza, O. and Balart, E. F. 2001. Community Structure of Reef Fish in Several Habitats of a Rocky Reef in the Gulf of California. Marine Ecology 22: 283-305</p> <p>2. Aburto-Oropeza, O. et al. 2015. A framework to assess the health of rocky reefs linking geomorphology, community assemblage, and fish biomass. Ecological Indicators 52: 353-361. <u>dx.doi.org/10.1016/j.ecolind.2014.12.006</u></p> <p>3. Acevedo-Cervantes A. et al. 2018. Geographic range and biology of Spinyeye Rockfish (<em>Sebastes spinorbis</em> Chen, 1975), an endemic species to the Gulf of California, Mexico. California Fish and Game 104: 148-153.</p> <p>4. Acevedo-Álvarez, E. A., G. Ruiz-Campos and O. Domínguez-Domínguez 2021 Population-level morphological variation of <em>Anisotremus interruptus</em> (Gill, 1862) (Perciformes: Haemulidae) in the Tropical Eastern Pacific, with the description of two new species. Zootaxa 4975: 141-158</p> <p>5. Ackerman JL, Bellwood DR (2000) Reef fish assemblages: a re-evaluation using enclosed rotenone stations Marine Ecology Progress Series 206:227-237. <u>doi:10.3354/meps206227</u></p> <p>6. Aguilar-Medrano, R. and Calderon-Aguilera, L.E. 2015. Redundancy and diversity of functional reef fish groups of the Mexican Eastern Pacific. Marine Ecology 2015: 1-15. <u>10.1111/maec.12253</u></p> <p>7. Allen, G.R. and Robertson, D.R. 1997. An annotated checklist of the fishes of Clipperton Atoll, tropical eastern Pacific. Rev. Biol. Trop. 45: 813-843</p> <p>8. Alvarez-Filip, L. and Reyes-Bonilla, H. 2006. Comparison of community structure and functional diversity of fishes at Cabo Pulmo coral reef, western Mexico between 1987 and 2003. Proceedings of 10th International Coral Reef Symposium 216-225</p> <p>9. Alzate, A. et al. 2012. New Records of Cryptobenthic Fishes in Coral Reef Habitats of Gorgona Island, Colombia, Tropical Eastern Pacific. Bol. Invest. Mar. Cost. 41: 229-235</p> <p>10. Alzate, A., Zapata, F.A., and Giraldo,A. 2014. A comparison of visual and collection-based methods for assessing community structure of coral reef fishes in the Tropical Eastern Pacific. Rev. Biol. Trop. 62: 359-371</p> <p>11. Anderson Jr., W.D. and Heemstra, P.C. 2012. Review of Atlantic and Eastern Pacific Anthiine Fishes (Teleostei: Perciformes: Serranidae), with Descriptions of Two New Genera. Trans. Am. Philos. Soc. 102: 204 pp</p> <p>12. Anderson, W.D., Jr. 2018. Annotated checklist of anthiadine fishes (Percoidei: Serranidae). Zootaxa 4475: 001-062. <u>https://doi.org/10.11646/zootaxa.4475.1.1</u></p> <p>13. Arias-Godínez, G. et al. 2021. The effect of coral reef degradation on the trophic structure of reef fishes from Bahía Culebra, North Pacific coast of Costa Rica. Journal of Coastal Conservation 25: 1-10. <a href="https://doi.org/10.1007/s11852-021-00802-x">https://doi.org/10.1007/s11852-021-00802-x</a></p> <p>14. Arreola-Robles JL, Elorduy-Garay JF 2002. Reef fish diversity in the region of La Paz, Baja California Sur, Mexico. Bull. Mar. Sci. 70: 1-8</p> <p>15. Auster, P.J. et al. 2016. Facilitative behavioral interactions between deepwater piscivores at Isla del Coco National Park and Las Gemelas Seamount, Costa Rica. Rev. Biol. Trop. 64: S187-S196.</p> <p>16. Auster PJ, Sánchez-Jiménez A, Rodríguez-Arrieta JA, Quesada AJ, Pérez C, Naranjo-Elizondo B, Blum S, Cortés J. (2016) Facilitative behavioral interactions between deepwater piscivores at Isla de Coco National Park and Las Gemelas Seamount, Costa Rica. Rev Biol Trop. 2016; 64 (Suppl 1):187-96.</p> <p>17. Auster, P.J. et al. 2019. Coordinated hunting behaviors of mixed-species groups of piscivores and associated species at Isla del Coco National Park (Eastern Tropical Pacific). Neotropical Ichthyology 17: 1-11. <u>10.1590/1982-0224-20180165</u></p> <p>18. Ayala Bocos, A., Fernández Rivera Melo, F.J., and Reyes Bonilla,H. 2018. Updated checklist of fishes at Cabo Pulmo reef, Gulf of California, Mexico. Rev. Mar. Cost 10: 9-29. <u>http://dx.doi.org/10.15359/revmar.10-1.1</u></p> <p>19. Ayala-Bocos, A. et al. 2015. New record of the frogfish <em>Fowlerichthys avalonis</em> (Actinopterygii, Antennariidae) at the oceanic Revillagigedo Archipelago, west Mexico. Marine Biodiversity Records 8: 1-4. <u>10.1017/S1755267215000275</u></p> <p>20. Balart, E. F. et al. 2006. Length–weight relationships of cryptic reef fishes from the southwestern Gulf of California, México. J. Appl. Ichthyol. 22: 316-318.</p> <p>21. Baldwin, C. C. and McCosker, J. E. 2001. Wrasses of the Galápagos Islands, with the description of a new deepwater species of Halichoeres (Perciformes: Labridae). Rev. Biol. Trop. 49: 89-100</p> <p>22. Baldwin CC, Tornabene L, Robertson DR (2018) Below the mesophotic. <em>Scientific Reports</em> 8:4920 <u> DOI:10.1038/s41598-018-23067-1</u></p> <p>23. Barjau E. et al. 2012. Estructura temporal y espacial de la comunidad de peces arrecifales de la Isla San José, Golfo de California, México. Rev. Biol. Trop. 60: 649-667</p> <p>24. Barjau E. et al. 2012. Changes in the taxonomic diversity of the reef fish community of San Jose´ Island, Gulf of California, Mexico. Biodivers Conserv 21: 3543–3554. 10.1007/s10531-012-0378-z</p> <p>25. 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Assessing a megadiverse but poorly known community of fishes in a tropical mangrove estuary through environmental DNA (eDNA) metabarcoding
<p>Biodiversity surveys are crucial for monitoring the status of threatened aquatic ecosystems, such as tropical estuaries and mangroves. Conventional monitoring methods are intrusive, time-consuming, substantially expensive, and often provide only rough estimates in complex habitats. An advanced monitoring approach, environmental DNA (eDNA) metabarcoding, is promising, although only few applications in tropical mangrove estuaries have been reported. In this study, we explore the advantages and limitations of an eDNA metabarcoding survey on the fish community of the Merbok Estuary (Peninsular Malaysia). COI and 12S eDNA metabarcoding assays collectively detected 178 species from 127 genera, 68 families, and 25 orders. Using this approach, significantly more species have been detected in the Merbok Estuary over the past decade (2010–2019) than in conventional surveys, including several species of conservation importance. However, we highlight three limitations: (1) in the absence of a comprehensive reference database the identities of several species are unresolved; (2) some of the previously documented specimen-based diversity was not captured by the current method, perhaps as a consequence of PCR primer specificity, and (3) the detection of non-resident species—stenohaline freshwater taxa (e.g., cyprinids, channids, osphronemids) and marine coral reef taxa (e.g., holocentrids, some syngnathids and sharks), not known to frequent estuaries, leading to the supposition that their DNA have drifted into the estuary through water movements. The community analysis revealed that fish diversity along the Merbok Estuary is not homogenous, with the upstream more diverse than further downstream. This could be due to the different landscapes or degree of anthropogenic influences along the estuary. In summary, we demonstrated the practicality of eDNA metabarcoding in assessing fish community and structure within a complex and rich tropical environment within a short sampling period. However, some limitations need to be considered and addressed to fully exploit the efficacy of this approach.</p>
Source Data for: Temperature, species identity and morphological traits predict carbonate excretion and mineralogy in tropical reef fishes
<p>Source Data underlying figures of the paper "Temperature, species identity and morphological traits predict carbonate excretion and mineralogy in tropical reef fishes" by Mattia Ghilardi, Michael A. Salter, Valeriano Parravicini, Sebastian C. A. Ferse, Tim Rixen, Christian Wild, Matthias Birkicht, Chris T. Perry, Alex Berry, Rod W. Wilson, David Mouillot, Sonia Bejarano</p>
Spatial genetic differentiation correlates with species assemblage turnover across tropical reef fish lineages
<p><strong>Aim:</strong> Evaluating the similarity of diversity patterns across micro- to macroevolutionary scales in natural communities, such as species-genetic diversity correlations (SGDC), may inform on processes shaping community assembly. However, whether SGDCs not only hold across communities but also across lineages has never been explored so far. Here we investigated SGDCs across co-distributed taxa for different spatial components (α, β, γ), and formally tested the influence of dispersal traits on β SGDCs. <strong>Location:</strong> Western Indian Ocean</p> <p><strong>Time period:</strong> 2016–2017</p> <p><strong>Major taxa studied:</strong> Tropical reef fish species with contrasting dispersal traits</p> <p><strong>Methods:</strong> Using ddRADseq single nucleotide polymorphism (SNP) data for 20 tropical reef fishes and distribution data of 2,446 species belonging to 12 families, we analysed the correlations between within-species genetic diversity and within-family species diversity (i.e., lineage diversity) for the three spatial components (α, β, γ SGDCs). We then related the strength of β-SGDCs per species to proxies of larval dispersal abilities.</p> <p><strong>Results:</strong> We detected positive and significant lineage-based SGDC only for the β component, i.e., the families showing the greatest level of species turnover among sites contains the species with the greatest levels of genetic differentiation. We showed that the Monsoon drift mainly explained the β diversity patterns at both intraspecific and interspecific levels. Higher β-SGDCs were found for species with short pelagic larval duration and weak larval swimming capacity.</p> <p><strong>Main conclusions:</strong> Our study reveals a strong correlation between genetic and species β diversity, a result explained by the presence of a 'soft' barrier and mediated by larval dispersal processes. This suggests that vicariance and dispersal limitation are major processes shaping β-diversity patterns from microevolutionary to macroevolutionary scales in tropical reef fishes.</p>
Patterns of reef fish taxonomic and functional diversity in the Eastern Tropical Pacific
<p class="MsoNormal">A core challenge in ecology is identifying the factors that determine species distribution and functional diversity of species assemblages. Reef fish are the most diverse group of vertebrates, form taxonomically rich and functionally diverse communities and represent a key source of food for humans. We examine regional distribution patterns of reef fish species richness and functional diversity and investigate how these are determined by historical, biogeographic, energetic, and anthropogenic factors. We compiled data from 3,312 underwater visual censuses (UVCs) performed at 122 locations comprising rocky and coral reefs along of the Eastern Tropical Pacific (ETP). We used Generalized Linear Mixed-effects Models (GLMM) implemented in a Bayesian framework to investigate whether distance from quaternary refugia, distance from mainland, shelf area, primary productivity, sea surface temperature, human population gravity and conservation status influence reef fish species richness and functional diversity in the ETP. Species richness and functional richness (FRic) peaked towards the center of the ETP and our null model suggests that FRic followed a spatial pattern than would be predicted by species richness. Additionally, functional evenness (FEve) was highest at higher latitudes whereas functional dispersion (FDis) was homogeneous throughout the ETP. Species richness was negatively influenced by shelf area and distance from the mainland but positively influenced by sea surface temperature and conservation status. FEve was influenced by human population gravity and FDis by shelf area, respectively. Reef fish<strong> </strong>species richness and functional diversity in the ETP exhibited a strong division within the region mainly mediated by sea surface temperature and human population gravity. Our results also suggest that dominant species in large areas share more common traits than dominant species in small areas. This study provides previously unknown regional patterns of reef fish functional diversity and new insights into how historical, biogeographic, energetic, and anthropogenic factors influence complementary biodiversity facets.</p>
Data from: Spatiotemporal patterns of trophic niche variation within and among species of tropical coastal fishes
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Patterns of reef fish taxonomic and functional diversity in the Eastern Tropical Pacific
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Data from: Endemic fish promote ecological structure in a tropical biodiversity hotspot
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Data from: Accelerated diversification explains the exceptional species richness of tropical characoid fishes
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Spatial genetic differentiation correlates with species assemblage turnover across tropical reef fish lineages
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