The discovery of fluorescent proteins has revolutionized experimental biology. Whereas the majority of fluorescent proteins have been identified from cnidarians, recently several fluorescent proteins have been isolated across the animal tree of life. Here we show that biofluorescence is not only phylogenetically widespread, but is also phenotypically variable across both cartilaginous and bony fishes, highlighting its evolutionary history and the possibility for discovery of numerous novel fluorescent proteins. Fish biofluorescence is especially common and morphologically variable in cryptically patterned coral-reef lineages. We identified 16 orders, 50 families, 105 genera, and more than 180 species of biofluorescent fishes. We have also reconstructed our current understanding of the phylogenetic distribution of biofluorescence for ray-finned fishes. The presence of yellow long-pass intraocular filters in many biofluorescent fish lineages and the substantive color vision capabilities of coral-reef fishes suggest that they are capable of detecting fluoresced light. We present species-specific emission patterns among closely related species, indicating that biofluorescence potentially functions in intraspecific communication and evidence that fluorescence can be used for camouflage. This research provides insight into the distribution, evolution, and phenotypic variability of biofluorescence in marine lineages and examines the role this variation may play.
Citation: Sparks JS, Schelly RC, Smith WL, Davis MP, Tchernov D, Pieribone VA, et al. (2014) The Covert World of Fish Biofluorescence: A Phylogenetically Widespread and Phenotypically Variable Phenomenon. PLoS ONE 9(1): e83259. https://doi.org/10.1371/journal.pone.0083259
Editor: Diego Fontaneto, Consiglio Nazionale delle Ricerche (CNR), Italy
Received: September 28, 2013; Accepted: October 31, 2013; Published: January 8, 2014
Copyright: © 2014 Sparks et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was supported by the American Museum of Natural History, City University of New York, National Science Foundation grants DEB-0444842, IOS-0749943, and DEB-1258141 to JSS, MCB-0920572 and DRL-1007747 to DFG, DEB-0732642 and DEB-1060869 to WLS, DEB-1257555 and DEB-1258141 to MPD, WLS, and JSS, National Institutes of Health (NIH) grants U24NS057631 and R01NS083875 to VAP and National Geographic Waitt Grants #W101-10 to DFG and #W214-12 to JSS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
The primarily monochromatic blue spectrum that characterizes large areas of the photic ocean provides a unique filtered-light environment for visual organisms. Compared to the terrestrial environment, marine organisms reside in a spectrally restricted visual domain. The red, orange, yellow, and green components of sunlight are selectively removed with depth resulting in a narrow, near-monochromatic, band of blue light between 470 and 480 nm . Spectrally restricted illumination in the ocean provides unique lighting conditions for organisms to exploit fluorescence to produce visual contrast and patterns. In the marine environment, biofluorescence is highly prevalent in cnidarians (particularly Anthozoans) , and also in a ctenophore , copepods , mantis shrimp , amphioxus  and some fishes . In addition, the photosynthetic apparatus associated with chlorophyll fluoresces red and provides a background of biofluorescence in areas of high algal growth on coral reefs.
Biofluorescence results from the absorption of electromagnetic radiation at one wavelength by an organism, followed by its reemission at a longer and lower energy wavelength, visually resulting in green, orange, and red emission coloration in marine organisms. Biofluorescence signaling has previously been reported in butterflies , parrots , spiders , and flowers , as well as a deep-sea siphonophore . In scleractinian corals, biofluorescence has been suggested to function in photoprotection , antioxidation , regulation of symbiotic dinoflagellates , photoacclimation , visual contrast , and coral health .
Whereas insight into the evolution and function of biofluorescence has greatly enhanced our knowledge of coral biology, little to nothing is known regarding the impact of biofluorescence on other organisms that thrive in coral-reef habitats, particularly those with advanced visual systems that could readily exploit fluorescent coloration and contrast. Investigating the evolution of biofluorescence across marine fishes is particularly appealing because they are visual animals, many of which possess yellow intraocular (lenses or cornea) filters , which function as long-pass filters and could enable enhanced perception of biofluorescence in the ocean. Worldwide, there are more than 8,000 species of fishes that inhabit coral reefs. Many reef fish species are known for their striking color patterns, whereas many others are cryptically patterned and appear well camouflaged. However, nearly nothing is known regarding the evolution or function of fluorescence in fishes. Only recently has a fluorescent protein, a novel fatty-acid-binding protein, been isolated from a vertebrate, a Japanese eel .
Here we report, for the first time, that biofluorescence is widespread throughout the tree of life for fishes, and it appears particularly common and phenotypically variable in marine lineages, especially cryptically patterned, well camouflaged coral-reef lineages. Our findings identify a widespread and previously unrecognized evolutionary phenomenon that provides new insights into the evolution of marine fishes and the function of light and visual systems in a marine environment, as well as providing a framework for the discovery of additional novel fluorescent proteins.
Research, collecting and export permits were obtained from the government of the Bahamas, from the Ministry of Fisheries and Ministry of Environment, Honiara, Solomon Islands, and from the Department of Environment, Cayman Islands Government. This study was carried out in strict accordance with the recommendations in the Guidelines for the Use of Fishes in Research of the American Fisheries Society and the American Museum of Natural History's Institutional Animal Care and Use Committee (IACUC). Fishes were collected via SCUBA, using both standard open circuit systems and closed circuit rebreathers, via the application of rotenone and quinaldine to a targeted variety of shallow to deep (mesophotic) habitats in each sampling location where collecting was permitted.
Taxonomic field surveys of biofluorescence in marine fishes were conducted during the following expeditions: Little Cayman Island, January 2011, working out of the Central Caribbean Marine Institute; the Exumas, Bahamas, May 2011 and December 2011, at the Perry Institute for Marine Science on Lee Stocking Island; and a taxonomically comprehensive survey conducted at numerous localities in the Solomon Islands (June–July, 2012 and September 2013). In addition, we have supplemented these field studies with specimens available in the aquarium trade and by imaging specimens at aquariums after hours (e.g., Mystic Aquarium and Institute for Exploration, Mystic, CT; Birch Aquarium, Scripps Institution of Oceanography, La Jolla, CA).
All collected specimens were placed on ice to preserve coloration and digitally imaged upon return to shore using Nikon D300s, D7000, or D800 DSLR cameras affixed with either a 60 or 105 mm Nikkor macro lens under white light. Fishes were subsequently scanned for fluorescence using bright LED light sources equipped with excitation filters and observed using emission filter glasses/goggles. All fluorescent fishes were then imaged (Fig. 1) using the “Fluorescent Macro Photography” protocol outlined below.
A, swell shark (Cephaloscyllium ventriosum); B, ray (Urobatis jamaicensis); C, sole (Soleichthys heterorhinos); D, flathead (Cociella hutchinsi); E, lizardfish (Synodus dermatogenys); F, frogfish (Antennarius maculatus); G, false stonefish (Scorpaenopsis diabolus); H, false moray eel (Kaupichthys brachychirus); I, false moray eel (Kaupichthys nuchalis); J, pipefish (Corythoichthys haematopterus); K, sand stargazer (Gillellus uranidea); L, goby (Eviota sp.); M, goby (Eviota atriventris); N, surgeonfish (Acanthurus coeruleus, larval); O, threadfin bream (Scolopsis bilineata).
The list and phylogenetic distribution of biofluorescence across cartilaginous and bony fishes presented in Figure 2 and Table S1 are the result of this survey work, and they also include data from  that specifically examined red fluorescence in some shallow, reef-associated fishes. In addition, we have summarized other accounts of biofluorescence in fishes from the popular literature (underwater photography magazines and websites) and available on the internet.
Family-level tree showing evolutionary relationships of ray-finned fishes inferred from maximum likelihood analysis of 221 species and six (one mitochondrial, five nuclear) genes. Note: Not all biofluorescent lineages are shown due to sampling limitations (see Table S1, Fig. S1).
Emission spectra were collected using an Ocean Optics USB2000+ miniature spectrometer (Dunedin, FL) equipped with a hand-held fiber optic probe (Ocean Optics ZFQ-12135). Excitation spectra were achieved during illumination with a band-pass filter (450–500 nm, Omega Optical, Inc., Brattleboro, VT, or Semrock, Inc., Rochester, NY). Emission spectra were recorded by applying the fiber optic probe to specific anatomical parts of the individual fish specimen exhibiting biofluorescence. This was repeated several times for each specimen to ensure the accuracy of measurements.
Fluorescent Macro Photography
Individual fish specimens were placed in a narrow photographic tank and held flat against a thin plate glass front. Fluorescent macro images [7360×4912 (Nikon D800); 4928×3264 (Nikon D7000); 2180×1800 pixel (Nikon D300S)] were produced in a dark room by covering the flash (Nikon SB 600, SB 800, or SB910) with interference bandpass excitation filters (Omega Optical, Inc., Brattleboro, VT; Semrock, Inc., Rochester, NY). Longpass (LP) and bandpass (BP) emission filters (Semrock) were attached to the front of the camera lens. A variety of excitation/emission filter pairs were tested on each sample to elicit the strongest fluorescence emission: excitation 450–500 nm, emission 514 LP; excitation 500–550 nm, emission 561 LP.
A majority of the DNA sequence data used in this study is from , but additional sequences were obtained from many studies –; the GenBank accession numbers for these sequences as well as our added GenBank accession numbers (KF768155-KF768177) can be found in Table S2. Mitochondrial and nuclear genes were aligned using the program MAFFT v6.0 with default parameters . The phylogenetic analysis presented herein had a total of 5,238 base pairs including: one mitochondrial gene (cytochrome oxidase I, 812 bps), and five protein-coding genes (glycosyltransferase gene, 732 bps; myosin heavy chain 6 alpha gene, 737 bps; pleiomorphic adenoma protein-like 2-like gene, 659 bps; recombination activating gene 1, 1403 bps; zic family member protein, 890 bps). For each maximum likelihood analysis, the dataset was partitioned by individual gene fragments. A model of molecular evolution was chosen by the program jMODELTEST v.2.1  with the best fitting model under the Akaike information criteria (AIC) for each individual gene partition assigned, including: cytochrome oxidase I (GTR+I+Γ), glycosyltransferase (GTR+ Γ), myosin heavy chain 6 alpha (GTR+I+Γ), pleiomorphic adenoma protein-like 2-like gene (GTR+I+Γ), recombination activating gene 1 (SYM+I+Γ), and zic family member protein (GTR+I+Γ). Maximum likelihood analyses were performed in GARLI v2.0 . Ten separate analyses were conducted, and the tree having the best likelihood score is presented here (Fig. S1, Fig. 2) to evaluate evolutionary relationships.
The results presented in this study are based upon ichthyofaunal surveys conducted during multiple expeditions to the Caribbean and tropical Western Pacific (2011–2013), analysis of living aquarium collections, and previous observations of biofluorescence from the literature. Biofluorescence is phylogenetically widespread and phenotypically variable in both cartilaginous (Chondrichthyes: sharks and rays) and bony (ray-finned: e.g, eels, lizardfishes, gobies, flatfishes) fishes (Figs. 1, 2, Table S1). We find biofluorescence to be most common and morphologically variable in cryptically pigmented and patterned marine lineages, including true eels (Anguilliformes), lizardfishes (Aulopiformes), scorpionfishes (Scorpaenoidei), blennies (Blennioidei), gobies (Gobioidei), and flatfishes (Pleuronectiformes) (Figs. 1, 2), groups that generally appear well camouflaged in the reef environment. With our initial surveys, we have already identified 16 orders, 50 families, 105 genera, and more than 180 species of biofluorescent fishes, and we have reconstructed our current understanding of the phylogenetic distribution of biofluorescence for ray-finned fishes (Fig. 2, Table S1).
We show that besides red fluorescence previously reported in shallow reef-associated fishes (e.g., , ), marine fishes also commonly exhibit green fluorescence, or combinations of green and red or orange fluorescence in unique, species-specific patterns (Figs. 1, 3). Biofluorescent patterning in fishes ranges from simple red, orange or green eye rings to striking, complex, species-specific patterns of interspersed fluorescent elements, frequently comprising multiple colors, on the head, jaws, fins, flank, and ventrum—and even bright fluorescence of the entire body (e.g., chlopsid eels; Fig. 1). Considerable interspecific variation in fluorescent emission patterns are recorded for members of the lizardfish genus Synodus (Fig. 3) and the goby genus Eviota (Fig. 1L, M), even among closely related species that appear nearly identical under white light (Fig. 3A, B).
Top panel: Interspecific variation in fluorescent emission pattern (from top: lateral, ventral, and dorsal views) in two congeneric and sympatric members of the lizardfish genus Synodus. A, S. synodus. B, S. saurus. Bottom panel: Interspecific variation in coloration and pigmentation pattern under white light (top: lateral; bottom: dorsal) in same two congeneric and sympatric members of the lizardfish genus Synodus. A, S. synodus. B, S. saurus.
We find biofluorescence to be widespread across cartilaginous and bony fishes, and we show that this evolutionary phenomenon is most common and phenotypically variable in cryptically colored and patterned marine fishes, such as eels, lizardfishes, blennies, scorpionfishes, gobies, and flatfishes (Figs. 1, 2). The repeated evolution of biofluorescence combined with phenotypically variable coloration (green, orange, red) and patterns in fishes may suggest a previously unrecognized role in communication, including mating behavior as has been observed in parrots . Fluorescence may be exploited in fishes to produce visual contrast and patterns in otherwise cryptically patterned or camouflaged species that blend in well on the reef in shallow sunlit waters.
A few instances of green biofluorescence have also been reported in deepwater (500–600 m) catsharks (Scyliorhinidae), lizardfishes (Aulopiformes: Chlorophthalmidae), and an unidentified ceriantharian (Cnidaria) –. The presence of biofluorescence in these deepwater taxa that spend their lives primarily in the dark, beyond the reach of the high-energy blue light necessary for excitation of fluorescence, is curious from a functional perspective. Biofluorescence in these taxa potentially represents the ancestral condition in lineages whose shallower water relatives also exhibit biofluorescence (Figs. 1, 2). Some bioluminescent (production and emission of light through a chemical reaction) deep-sea organisms have previously been shown to exhibit biofluorescence through a coupling of both bioluminescent and biofluorescent systems. A heavily studied example is the crystal jellyfish (Aequorea victoria) in which the bioluminescent system (aequorin) produces blue light that directly excites green fluorescent protein (GFP) to emit green light , likely via a Förster energy transfer process . In another example, the deep-sea loose-jaw dragonfish (Malacosteus) emits red light through biofluorescence via the absorption of blue bioluminescent light produced by the fish, which is reemitted by a chlorophyll-like compound as red light and is hypothesized to aid in predation . In addition, some deep-sea siphonophores also utilize bioluminescent light to excite red biofluorescence .
Shallow water bony fishes generally exhibit good color vision –, a result of living in a visually complex environment; in contrast, fishes occurring in deeper water exhibit limited color vision due to a simpler (blue-shifted) visual environment. Recent evidence indicates that sharks and rays also exhibit color vision –. Many of the fishes we find to exhibit biofluorescence (Figs. 1, 2), such as sharks, lizardfishes, scorpionfishes, labrids (wrasses), and flatfishes, also possess yellow intraocular filters . Yellow intraocular filters in the lenses and corneas of certain fishes function as long-pass filters, thus enabling the species that possess them to visualize and potentially exploit fluorescence to enhance visual contrast and patterns that are unseen to other fishes and predators that lack this visual specialization.
It has been hypothesized that some polarization sensitive cephalopods communicate via “private” polarized light signals that allow them to simultaneously remain camouflaged to predators  and exploit a “hidden” communication mechanism between conspecifics . Cephalopods possess a rhabdomeric visual system that enables detection of linearly polarized light and they are able to produce polarized skin patterns using iridophores , whereas many of their predators (marine mammals and some fishes) are not sensitive to the polarization of light . Likewise, fishes that possess the necessary yellow intraocular filters for visualizing biofluorescence could be exploiting a similar “hidden” light signal for a similar functional role. We found that biofluorescent patterning was especially prominent in cryptically patterned fishes, and that many of these lineages also possess yellow long-pass intraocular filters that could enable visualization of such patterns (Figs. 1, 2).
In recent years, biofluorescence has also been found in patchy occurrences in some copepods  and mantis shrimp (phylum Arthropoda) , amphioxus (phylum Chordata) , and a species of comb jelly (phylum Ctenophora) . Biofluorescence has been shown to enhance signaling in the mantis shrimp, Lysiosquillina glabriuscula, a species identified to have a complex system of color visualization . Additionally, there have been reports of fluorescence signaling in butterflies , parrots , spiders , and flowers , as well as in a deep-sea siphonophore .
The phylogeny presented in Figure 1 indicates that biofluorescence is phylogenetically widespread and phenotypically variable across ray-finned fishes (Actinopterygii) in terms of the diversity of patterns observed (Figs. 1, 3), emission spectra (Fig. 4), and intensity. We observed distinct variation among lineages and pronounced interspecific variation in emission patterns in closely related taxa that otherwise look nearly identical under white light. For example, closely related lizardfish species within the genus Synodus exhibit fluorescence patterns that are notably more distinct than their pigmentation patterns appear under daylight/white light (Fig. 3). Considerable interspecific fluorescent pattern variation is also observed across species in the goby genus Eviota (Fig. 1L, M) and for chlopsid eels (Anguilliformes: Chlopsidae; Fig. 1H, I). Our observations indicate that flatfishes exhibit distinctly different fluorescent patterns on their sighted and blind surfaces (fluorescence on the sighted side being primarily red (Fig. 1B), whereas the blind side generally fluoresces green), which is intriguing given that flatfishes are well known to flash their blind sides to each other during mating rituals. Individuals of some other species were found to exhibit both alternating red and green fluorescent patterns (e.g., Fig. 1K), whereas in other lineages, only the larval forms were observed to fluoresce (e.g., Fig. 1N, acanthurids). Such observations in combination with pronounced interspecific variability in fluorescence emission pattern in otherwise similarly patterned taxa suggest that intraspecific communication is a function of biofluorescence in marine fishes, as has been shown in other organisms with complex visual systems (e.g., ). In addition, certain marine fishes (e.g., , ) spawn synchronously surrounding the full moon. Moonlight illumination in shallow ocean waters could potentially provide the appropriate excitation energy for green and red biofluorescence in fishes, and as a result, species-specific biofluorescent patterning may provide an added layer of species recognition during the spawning phase, when fishes are particularly vulnerable to predation.
Key to species sampled: Ray (family Urotrygonidae, genus Urobatis); Eel (family Chlopsidae, genus Kaupichthys); Scorpionfish (family Scorpaenidae, genus Scorpeana); Goby (family Gobiidae, genus Eviota).
In addition, we present evidence that some fish lineages might be utilizing fluorescence as a means of camouflage in specific marine environments (Fig. 5; Videos S1, S2). Red and far-red biofluorescence is a ubiquitous feature of photosynthetic organisms due to the properties of chlorophyll and other photosynthetic pigment complexes. The photosynthetic apparatus associated with chlorophyll fluoresces red and provides a background of biofluorescence in areas of algal growth. Apart from photosynthetic organisms, red biofluorescence also occurs due to fluorescent proteins . In two species of red biofluorescent scorpionfishes that we imaged, individuals were observed residing on top of a patch of red fluorescing algae (Fig. 5A). We also recorded a bream (Scolopsis) with green fluorescent patterns on its nape swimming within a green fluorescing Acropora coral outcrop (Fig. 5B). It would appear that under fluorescent conditions, these species are particularly well camouflaged in the specific environments in which they were imaged.
(A) A red fluorescing scorpionfish, Scorpaenopsis papuensis, perched on red fluorescing algae. (B) A green fluorescing nemipterid (bream), Scolopsis bilineata, near a green fluorescing Acropora sp. coralhead.
In summary, the widespread nature of biofluorescence in both cartilaginous and bony, ray-finned marine fishes, coupled with the presence of yellow intraocular filters in many biofluorescent lineages that would permit the visualization of fluorescent emissions, is intriguing. Biofluorescence is most prominent and phenotypically variable in cryptically patterned, well-camouflaged lineages (Figs. 1, 2) that otherwise blend in with their surroundings. Coupled with observations of notably distinct fluorescent emission patterns among closely related species (including sister species) that otherwise strongly resemble each other under white light/daylight (Figs. 2, 3), suggests a intraspecific communication/species recognition function. Conversely, we observed species that appear to blend in with their surroundings under fluorescent lighting conditions (Fig. 5), and that could theoretically exploit biofluorescence as a means of camouflage to either avoid being detected by potential prey or to elude predators. Based on these data, the possibility exists that marine fishes are using biofluorescence for a variety of functions, including communication (species recognition, mating), predator avoidance, and potentially even prey attraction/predation. The broad phylogenetic distribution of biofluorescence across bony fishes is consistent with its repeated independent evolution, and its importance in the diversification of marine fishes remains to be explored. As Johnsen  justly notes, the field of biofluorescence is wide open for study and there have been far too few studies to date, most of which have focused on cnidarians. With the recent discovery of a novel fluorescent protein from a vertebrate , we expect that biofluorescence in marine fishes will be the subjects of many future studies, from the level of proteins to whole organisms in their environment.
Maximum likelihood topology of the evolutionary relationships of ray-finned fishes inferred from the analysis of 221 species (representing more than 145 families), with six gene fragments (one mitochondrial, five nuclear).
Biofluorescent fishes known to date. Taxa are listed alphabetically by Order (column 1), Family (column 2), and Species (column 3). Columns 4 (red) and 5 (green) contain filled circles corresponding to the observed color of fluoresced light. Column 6 gives AMNH catalog numbers. Taxa indicated with an * are not included in the phylogenetic reconstruction (Fig. 2).
Supplementary video to accompany Fig. 5A showing a red fluorescing scorpionfish, Scorpaenopsis papuensis, perched on red fluorescing algae in its natural habitat. Video captured with a Red Epic video camera at night in the Solomon Islands.
Supplementary video to accompany Fig. 5B showing a green fluorescing nemipterid (bream), Scolopsis bilineata, swimming near a green fluorescing Acropora sp. coralhead. Video captured with a Red Epic video camera at night in the Solomon Islands.
We are grateful to Ray and Barbara Dalio and the Dalio Family Foundation, Fabio Amador and Dominique Rissolo of the National Geographic Society/Waitt Program, Zipolo Habu Resort and Dive Gizo, Solomon Islands, Perry Institute for Marine Science, Lee Stocking Island, and Central Caribbean Marine Institute, Little Cayman Island, for providing facilities, boats, submersibles, and logistical support. Research, collecting and export permits were obtained from the government of the Bahamas, from the Ministry of Fisheries and Ministry of Environment, Honiara, Solomon Islands, and from the Department of Environment, Cayman Islands Government. Thanks also to D. Harrington and T. Romano at Mystic Aquarium and N. Hillgarth and R. Elkus at Birch Aquarium (UCSD) for access to their collections; to M. Lombardi and J. Godfrey for deep diving assistance; and to the J.B. Pierce Lab machine shop for equipment design.
Conceived and designed the experiments: JSS RCS WLS MPD DT VAP DFG. Performed the experiments: JSS RCS WLS MPD DT VAP DFG. Analyzed the data: JSS RCS WLS MPD VAP DFG. Contributed reagents/materials/analysis tools: JSS RCS WLS MPD VAP DFG. Wrote the paper: JSS RCS WLS MPD VAP DFG.
- 1. Jerlov NG (1968) Optical Oceanography. New York: American Elsevier Publ. Co. 194 p.
- 2. Gruber DF, Kao HT, Janoschka S, Tsai J, Pieribone VA (2008) Patterns of fluorescent protein expression in scleractinian corals. Biol Bull 215: 143–154.
- 3. Haddock SHD, Mastroianni N, Christianson LM (2010) A photoactivatable green-fluorescent protein from the phylum Ctenophora. Proc Roy Soc of Lond, Ser B 277: 1155–1160.
- 4. Shagin DA, Barsova EV, Yanushevich YG, Fradkov AF, Lukyanov KA, et al. (2004) GFP-like proteins as ubiquitous metazoan superfamily: Evolution of functional features and structural complexity. Mol Biol Evol 21: 841–850.
- 5. Mazel CM, Cronin TW, Caldwell RL, Marshall NJ (2004) Fluorescent enhancement of signaling in a mantis shrimp. Science 303: 51.
- 6. Deheyn DD, Kubokawa K, McCarthy JK, Murakami A, Porrachia M, et al. (2007) Endogenous green fluorescent protein (GFP) in amphioxus. Biol Bull 213: 95–100.
- 7. Michiels NK, Anthes N, Hart NS, Herler J, Meixner AJ, et al. (2008) Red fluorescence in reef fish: A novel signalling mechanism? BMC Ecol 8: 16.
- 8. Vukusic P, Hooper I (2005) Directionally controlled fluorescence emission in butterflies. Science 310: 1151.
- 9. Arnold KE, Owens IPF, Marshall NJ (2002) Fluorescent signaling in parrots. Science 295: 92.
- 10. Andrews K, Reed SM, Masta SE (2007) Spiders fluoresce variably across many taxa. Biol Lett 3: 265–267.
- 11. Gandía-Herrero F, García-Carmona F, Escribano J (2005) Botany: Floral fluorescence effect. Nature 437: 334.
- 12. Haddock SHD, Dunn CW, Pugh PR, Schnitzler CE (2005) Bioluminescent and red-fluorescent lures in a deep-sea siphonophore. Science 309: 263.
- 13. Salih A, Larkum A, Cox G, Kühl M, Hoegh-Guldberg O (2000) Fluorescent pigments in corals are photoprotective. Nature 408: 850–853.
- 14. Bou-Abdallah F, Chasteen ND, Lesser MP (2006) Quenching of superoxide radicals by green fluorescent protein. Biochim Biophys Acta 1760: 1690–1695.
- 15. Field SF, Bulina MY, Kelmanson IV, Bielawski JP, Matz MV (2006) Adaptive evolution of multicolored fluorescent proteins in reef-building corals. J Mol Evol 62: 332–339.
- 16. Roth MS, Latz MI, Goericke R, Deheyn DD (2010) Green fluorescent protein regulation in the coral Acropora yongei during photoacclimation. (2010). J Exp Biol 213: 3644–3655.
- 17. Roth MS, Deheyn DD (2013) Effects of cold stress and heat stress on coral fluorescence in reef-building corals,. Sci Rep 3: 1421.
- 18. Heinermann PH (1984) Yellow intraocular filters in fishes. Exp Biol 43: 127–147.
- 19. Kumagai A, Ando R, Miyatake H, Greimel P, Kobayashi T, et al. (2013) A bilirubin-inducible fluorescent protein from eel muscle. Cell 153: 1602–1611.
- 20. Near TJ, Eytan RI, Dornburg A, Kuhn KL, Moore JA, et al. (2012) Resolution of ray-finned fish phylogeny and timing of diversification. Proc Natl Acad Sci U S A 109: 13698–13703.
- 21. Wainwright PC, Smith WL, Price SA, Tang KL, Sparks JS, et al. (2012) The evolution of pharyngognathy: A phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond. Syst Biol 61: 1001–1027.
- 22. April J, Mayden RL, Hanner RH, Bernatchez L (2011) Genetic calibration of species diversity among North America's freshwater fishes. Proc Natl Acad Sci U S A 108: 10602–10607.
- 23. Aquilino SVL, Tango JM, Fontanilla IKC, Pagulayan RC, Basiao ZU, et al. (2011) DNA barcoding of the ichthyofauna of Taal Lake, Philippines. Mol Ecol Res 11: 612–619.
- 24. Arnold RJ, Pietsch TW (2012) Evolutionary history of frogfishes (Teleostei: Lophiiformes: Antennariidae): A molecular approach. Mol Phylogenet Evol 62: 117–129.
- 25. Asgharian H, Sahafi HH, Ardalan AA, Shekarriz S, Elahi E (2011) Cytochrome c Oxidase Subunit 1 barcode data of fish of the Nayband National Park in the Persian Gulf and analysis using meta-data flag several cryptic species. Mol Ecol Res 11: 461–472.
- 26. Quenouille B, Bermingham E, Planes S (2004) Molecular systematics of the damselfishes (Teleostei: Pomacentridae): Bayesian phylogenetic analyses of mitochondrial and nuclear DNA sequences. Mol Phylogenet Evol 31: 66–88.
- 27. Costa FO, Landi M, Martins R, Costa MH, Costa ME, et al. (2012) A ranking system for reference libraries of DNA barcodes: Application to marine fish species from Portugal. PloS One 7: e35858.
- 28. Crête-Lafrenière A, Weir LK, Bernatchez L (2012) Framing the Salmonidae family phylogenetic portrait: A more complete picture from increased taxon sampling. PloS One 7: e46662.
- 29. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD (2005) DNA barcoding Australia's fish species. Phil Trans Roy Soc London B, Biol Sci 360: 1847–1857.
- 30. Davis MP (2010) Evolutionary relationships of the Aulopiformes (Euteleostei: Cyclosquamata): A molecular and total evidence approach. In: J. S. Nelson, H.-P. Schultze and M. V. H. Wilson, editors. Origin and Phylogenetic Interrelationships of Teleosts. München: Verlag Dr. F. Pfeil. pp. 431–470.
- 31. Dunlap PV, Ast JC, Kimura S, Fukui A, Yoshino T, et al. (2007) Phylogenetic analysis of host-symbiont specificity and codivergence in bioluminescent symbioses. Cladistics 23: 507–532.
- 32. Espiñeira M, González-Lavín N, Vieites JM, Santaclara FJ (2008) Authentication of anglerfish species (Lophius spp) by means of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and forensically informative nucleotide sequencing (FINS) methodologies. J Agricult Food Chem 56: 10594–10599.
- 33. Santini F, Sorenson L, Marcroft T, Dornburg A, Alfaro ME (2013) A multilocus molecular phylogeny of boxfishes (Aracanidae, Ostraciidae; Tetraodontiformes). Mol Phylogenet Evol 66: 153–160.
- 34. Fu C, Guo L, Xia R, Li J, Lei G (2012) A multilocus phylogeny of Asian noodlefishes Salangidae (Teleostei: Osmeriformes) with a revised classification of the family. Mol Phylogenet Evol 62: 848–855.
- 35. Guo L, Li J, Wang Z, Fu C (2011) Phylogenetic relationships of noodle-fishes (Osmeriformes: Salangidae) based on four mitochondrial genes. Acta Hydrobiol Sinica 35: 449–459.
- 36. Holcroft NI (2004) A molecular test of alternative hypotheses of tetraodontiform (Acanthomorpha: Tetraodontiformes) sister group relationships using data from the RAG1 gene. Molecular Mol Phylogenet Evol 32: 749–760.
- 37. Holcroft NI, Wiley EO (2008) Acanthuroid relationships revisited: a new nuclear gene-based analysis that incorporates tetraodontiform representatives. Ichthyol Res 55: 274–283.
- 38. Hubert N, Hanner R, Holm E, Mandrak NE, Taylor E, et al. (2008) Identifying Canadian freshwater fishes through DNA barcodes. PLoS One 3: e2490.
- 39. Hubert N, Meyer CP, Bruggemann HJ, Guerin F, Komeno RJL, et al. (2012) Cryptic diversity in Indo-Pacific coral-reef fishes revealed by DNA-barcoding provides new support to the centre-of-overlap hypothesis. PLoS One 7: e28987.
- 40. Ilves KL, Taylor EB (2007) Are Hypomesus chishimaensis and H. nipponensis (Osmeridae) distinct species? A molecular assessment using comparative sequence data from five genes. Copeia 2007: 180–185.
- 41. Inoue JG, Miya M, Tsukamoto K, Nishida M (2003) Evolution of the deep-sea gulper eel mitochondrial genomes: Large-scale gene rearrangements originated within the eels. Mol Biol Evol 20: 1917–1924.
- 42. Inoue JG, Miya M, Tsukamoto K, Nishida M (2003) Basal actinopterygian relationships: A mitogenomic perspective on the phylogeny of the “ancient fish”. Mol Phylogenet Evol 26: 110–120.
- 43. Inoue JG, Miya M, Tsukamoto K, Nishida M (2004) Mitogenomic evidence for the monophyly of elopomorph fishes (Teleostei) and the evolutionary origin of the leptocephalus larva. Mol Phylogenet Evol 32: 274–286.
- 44. Ishiguro N, Miya M, Nishida M (2001) Complete mitochondrial DNA sequence of Ayu Plecoglossus altivelis. Fish Sci 67: 474–481.
- 45. Ishiguro NB, Miya M, Nishida M (2003) Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of the “Protacanthopterygii”. Mol Phylogenet Evol 27: 476–488.
- 46. Jaafar TNAM, Taylor MI, Nor SAM, de Bruyn M, Carvalho GR (2012) DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleostei: Perciformes). PloS One 7: e49623.
- 47. Kaeding AJ, Ast JC, Pearce MM, Urbanczyk H, Kimura S, et al. (2007) Phylogenetic diversity and cosymbiosis in the bioluminescent symbioses of “Photobacterium mandapamensis”. App Environ Microbiol 73: 3173–3182.
- 48. Lakra WS, Verma MS, Goswami M, Lal KK, Mohindra V, et al. (2011) DNA barcoding Indian marine fishes. Mol Ecol Res 11: 60–71.
- 49. Lavoué S, Miya M, Inoue JG, Saitoh K, Ishiguro NB, et al. (2005) Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: Implications for higher-level relationships within the Otocephala. Mol Phylogenet Evol 37: 165–177.
- 50. Lavoué S, Miya M, Moritz T, Nishida M (2012) A molecular timescale for the evolution of the African freshwater fish family Kneriidae (Teleostei: Gonorynchiformes). Ichthyol Res 59: 104–112.
- 51. Lavoué S, Miya M, Poulsen JY, Møller PR, Nishida M (2008) Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences. Mol Phylogenet Evol 47: 1111–1121.
- 52. Li C, Ortí G (2007) Molecular phylogeny of Clupeiformes (Actinopterygii) inferred from nuclear and mitochondrial DNA sequences. Mol Phylogenet Evol 44: 386–398.
- 53. Li C, Ortí G, Zhang G, Lu G (2007) A practical approach to phylogenomics: The phylogeny of ray-finned fish (Actinopterygii) as a case study. BMC Evol Biol 7: 44.
- 54. Li C, Ricardo B-R, Smith WL, Ortí G (2011) Monophyly and interrelationships of Snook and Barramundi (Centropomidae sensu Greenwood) and five new markers for fish phylogenetics. Mol Phylogenet Evol 60: 463–471.
- 55. López JA, Chen W-J, Ortí G (2004) Esociform phylogeny. Copeia 2004.
- 56. Marie AD, Van Herwerden L, Choat JH, Hobbs JA (2007) Hybridization of reef fishes at the Indo-Pacific biogeographic barrier: A case study. Coral Reefs 26: 841–850.
- 57. Mecklenburg CW, Møller PR, Steinke D (2011) Biodiversity of arctic marine fishes: taxonomy and zoogeography. Mar Biodivers 41: 109–140.
- 58. Miya M, Holcroft NI, Satoh TP, Yamaguchi M, Nishida M, et al. (2007) Mitochondrial genome and a nuclear gene indicate a novel phylogenetic position of deep-sea tube-eye fish (Stylephoridae). Ichthyol Res 54: 323–332.
- 59. Miya M, Kawaguchi A, Nishida M (2001) Mitogenomic exploration of higher teleostean phylogenies: A case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences. Mol Biol and Evol 18: 1993–2009.
- 60. Moritz T, Britz R, Linsenmair KE (2006) Cromeria nilotica and C. occidentalis, two valid species of the African freshwater fish family Kneriidae (Teleostei: Gonorynchiformes). Ichythol Explor Freshwater 17: 65–72.
- 61. Hubert N, Delrieu-Trottin E, Irisson JO, Meyer C, Planes S (2010) Identifying coral reef fish larvae through DNA barcoding: A test case with the families Acanthuridae and Holocentridae. Mol Phylogenet Evol 55: 1195–1203.
- 62. Near TJ, Dornburg A, Eytan RI, Keck BP, Smith WL, et al. (2013) Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes. Proc Natl Acad Sci U S A 110: 12738–12743.
- 63. Near TJ, Dornburg A, Kuhn KL, Eastman JT, Pennington JN, et al. (2012) Ancient climate change, antifreeze, and the evolutionary diversification of Antarctic fishes. Proc Natl Acad Sci U S A 109: 3434–3439.
- 64. Near TJ, Sandel M, Kuhn KL, Unmack PJ, Wainwright PC, et al. (2012) Nuclear gene-inferred phylogenies resolve the relationships of the enigmatic Pygmy Sunfishes, Elassoma (Teleostei: Percomorpha). Mol Phylogenet Evol 63: 388–395.
- 65. Niemiller ML, Near TJ, Fitzpatrick BM (2012) Delimiting species using multilocus data: Diagnosing cryptic diversity in the southern cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae). Evol 66: 846–866.
- 66. Ribeiro AO, Caires RA, Mariguela TC, Pereira LH, Hanner R, et al. (2012) DNA barcodes identify marine fishes of São Paulo State, Brazil. Mol Ecol Res 12: 1012–1020.
- 67. Roa-Varón A, Ortí G (2009) Phylogenetic relationships among families of Gadiformes (Teleostei, Paracanthopterygii) based on nuclear and mitochondrial data. Mol Phylogenet Evol 52: 688–704.
- 68. Saitoh K, Miya M, Inoue JG, Ishiguro NB, Nishida M (2003) Mitochondrial genomics of ostariophysan fishes: Perspectives on phylogeny and biogeography. J Mol Evol 56: 464–472.
- 69. Saitoh K, Sado T, Mayden RL, Hanzawa N, Nakamura K, et al. (2006) Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The first evidence toward resolution of higher-level relationships of the world's largest freshwater fish clade based on 59 whole mitogenome sequences. J Mol Evol 63: 826–841.
- 70. Smith PJ, Steinke D, Dettai A, McMillan P, Welsford D, et al. (2012) DNA barcodes and species identifications in Ross Sea and Southern Ocean fishes. Polar Biol 35: 1297–1310.
- 71. Sparks JS (2003) Taxonomic status of the Malagasy cichlid Ptychochromis grandidieri (Teleostei: Cichlidae), including a molecular phylogenetic analysis of the ptychochromine cichlids. Ichthyol Explor Freshwaters 14: 317–328.
- 72. Sparks JS, Dunlap PV, Smith WL (2005) Evolution and diversification of a sexually dimorphic luminescent system in ponyfishes (Teleostei: Leiognathidae), including diagnoses for two new genera. Cladistics 21: 305–327.
- 73. Sparks JS, Smith WL (2004) Phylogeny and biogeography of cichlid fishes (Teleostei: Perciformes: Cichlidae). Cladistics 20: 501–517.
- 74. Sparks JS, Smith WL (2004) Phylogeny and biogeography of the Malagasy and Australasian rainbowfishes (Teleostei: Melanotaenioidei): Gondwanan vicariance and evolution in freshwater. Mol Phylogenet Evol 33: 719–734.
- 75. Steinke D, Zemlak TS, Hebert PDN (2009) Barcoding Nemo: DNA-based identifications for the ornamental fish trade. PLoS One 4: e6300.
- 76. Thacker CE (2009) Phylogeny of Gobioidei and placement within Acanthomorpha, with a new classification and investigation of diversification and character evolution. Copeia 2009: 93–104.
- 77. Thacker CE, Hardman MA (2005) Molecular phylogeny of basal gobioid fishes: Rhyacichthyidae, Odontobutidae, Xenisthmidae, Eleotridae (Teleostei: Perciformes: Gobioidei). Mol Phylogenet Evol 37: 858–871.
- 78. Varela AI, Ritchie PA, Smith PJ (2012) Low levels of global genetic differentiation and population expansion in the deep-sea teleost Hoplostethus atlanticus revealed by mitochondrial DNA sequences. Mar Biol 159: 1049–1060.
- 79. Ward RD, Costa FO, Holmes BH, Steinke D (2008) DNA barcoding of shared fish species from the North Atlantic and Australasia: Minimal divergence for most taxa, but Zeus faber and Lepidopus caudatus each probably constitute two species. Aquat Biol 3: 71–78.
- 80. Weigt LA, Baldwin CC, Driskell A, Smith DG, Ormos A, et al. (2012) Using DNA barcoding to assess Caribbean reef fish biodiversity: Expanding taxonomic and geographic coverage. PloS One 7: e41059.
- 81. Yamanoue Y, Miya M, Matsuura K, Katoh M, Sakai H, et al. (2004) Mitochondrial genomes and phylogeny of the ocean sunfishes (Tetraodontiformes: Molidae). Ichthyol Res 51: 269–273.
- 82. Yamanoue Y, Miya M, Matsuura K, Yagishita N, Mabuchi K, et al. (2007) Phylogenetic position of tetraodontiform fishes within the higher teleosts: Bayesian inferences based on 44 whole mitochondrial genome sequences. Mol Phylogenet Evol 45: 89–101.
- 83. Zhang J, Hanner R (2011) DNA barcoding is a useful tool for the identification of marine fishes from Japan. Biochem Syst Ecol 39: 31–42.
- 84. Zhang J, Hanner R (2012) Molecular approach to the identification of fish in the South China Sea. PloS One 7: e30621.
- 85. Katoh T (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9: 286–298.
- 86. Posada D (2008) Jmodeltest: Phylogenetic model averaging. Mol Biol Evol 25: 1253–1256.
- 87. Zwickl DJ (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion, PhD Thesis, University of Texas, Austin.
- 88. Wucherer MF, Michiels NK (2012) A fluorescent chromatophore changes the level of fluorescence in a reef fish. PLoS One 7(6): e37913.
- 89. Vogt A, D'Angelo C, Oswald F, Denzel A, Mazel CH, et al. (2008) A green fluorescent protein with photoswitchable emission from the deep sea. PLoS One 3(11): e3766.
- 90. Shimomura O, Johnson FJ, Saiga Y (1962) Extraction, purification and properties of aequorin, a bioluminescent protein from the luminous hydromedusan, Aequorea. J Cell Comp Physiol 59: 223–239.
- 91. Morin JG, Hastings JW (1971) Energy transfer in a bioluminescent system. J Cell Physiol 77: 313–318.
- 92. Douglas RH, Partridge JC, Dulai K, Hunt D, Mullineaux CW, et al. (1998) Dragon fish see using chlorophyll. Nature 393: 423–424.
- 93. Losey GS, McFarland WN, Loew ER, Zamzow JP, Nelson PA, et al. (2003) Visual biology of Hawaiian coral reef fishes. I. Ocular transmission and retinal sensitivity. Copeia 2003: 433–454.
- 94. Siebeck UE, Wallis GM, Litherland L (2008) Colour vision in coral reef fish. J Exp Biol 211: 354–360.
- 95. Theiss SM, Lisney TJ, Collin SP, Hart NS (2007) Colour vision and visual ecology of the blue-spotted maskray, Dasyatis kuhlii Müller & Henle, 1814. J Comp Phys, Ser A 193: 67–79.
- 96. Van-Eyk SM, Siebeck UE, Champ CM, Marshall J, Hart NS (2011) Behavioural evidence for colour vision in an elasmobranch. J Exp Biol 214: 4186–4192.
- 97. Mäthger LM, Shashar N, Hanlon RT (2009) Do cephalopods communicate using polarized light reflections from their skin? J Exp Biol 212: 2133–2140.
- 98. Marshall NJ (1999) Behavioural evidence for polarization vision in stomatopods reveals a potential channel for communication. Curr Biol 9: 755–758.
- 99. Shashar N, Hanlon RT (1997) Squids (Loligo pealei and Euprymna scolopes) can exhibit polarized light patterns produced by their skin. Biol Bull 193: 207–208.
- 100. Hawryshyn CW (1992) Polarization vision in fish. Am Sci 80: 164–75.
- 101. Lobel PS (1978) Diel, lunar, and seasonal periodicity in the reproductive behavior of the pomacanthid fish, Centropyge potteri, and some other reef fishes in Hawaii. Pac Sci 32: 193–207.
- 102. Takemura A, Rahman MdS, Nakamura S, Park YJ, Takano K (2004) Lunar cycles and reproductive activity in reef fishes with particular attention to rabbitfishes. Fish and Fisheries 5: 317–328.
- 103. Johnsen S (2012) The Optics of Life: A Biologist's Guide to Light in Nature. Princeton: Princeton University Press. 360 p.