Editing Fluorescence (section)

== In nature ==
[[File:Fluorescent Coral Movie.gif|thumb|Fluorescent coral]]
{{main|Fluorescence in the life sciences}}
There are many natural compounds that exhibit fluorescence, and they have a number of applications. Some deep-sea animals, such as the [[greeneye]], have fluorescent structures.

=== Compared to bioluminescence and biophosphorescence ===
==== Fluorescence ====
Fluorescence is the phenomenon of absorption of [[electromagnetic radiation|electromagnetic]] radiation, typically from ultraviolet or [[visible light]], by a molecule and the subsequent emission of a photon of a lower energy (smaller frequency, longer wavelength). This causes the light that is emitted to be a different color than the light that is absorbed. Stimulating light excites an [[electron]] to an excited state. When the molecule returns to the ground state, it releases a photon, which is the fluorescent emission. The excited state lifetime is short, so emission of light is typically only observable when the absorbing light is on. Fluorescence can be of any wavelength but is often more significant when emitted photons are in the visible spectrum. When it occurs in a living organism, it is sometimes called biofluorescence. Fluorescence should not be confused with bioluminescence and biophosphorescence.<ref name="Fluorescence in marine organisms">{{cite web|title=Fluorescence in marine organisms|url=http://gestaltswitchexpeditions.com/fluorescence-in-marine-orga/|website=Gestalt Switch Expeditions|url-status=dead|archive-url=https://web.archive.org/web/20150221070425/http://www.gestaltswitchexpeditions.com/fluorescence-in-marine-orga/|archive-date=21 February 2015}}</ref> Pumpkin toadlets that live in the Brazilian Atlantic forest are fluorescent.<ref>{{Cite news|url=https://www.business-standard.com/article/pti-stories/fluorescence-discovered-in-tiny-brazilian-frogs-119032900584_1.html|title=Fluorescence discovered in tiny Brazilian frogs|agency=Press Trust of India|date=2019-03-29|work=Business Standard India|access-date=2019-03-30|archive-date=30 March 2019|archive-url=https://web.archive.org/web/20190330124158/https://www.business-standard.com/article/pti-stories/fluorescence-discovered-in-tiny-brazilian-frogs-119032900584_1.html|url-status=live}}</ref>

==== Bioluminescence ====
[[Bioluminescence]] differs from fluorescence in that it is the natural production of light by chemical reactions within an organism, whereas fluorescence is the absorption and reemission of light from the environment.<ref name="Fluorescence in marine organisms"/> [[Firefly|Fireflies]] and [[anglerfish]] are two examples of bioluminescent organisms.<ref>{{cite web|url=https://earthnworld.com/top-10-amazing-bioluminescent-animals-planet-earth/|title=Top 10 Amazing Bioluminescent Animals on Planet Earth|last=Utsav|date=2017-12-02|website=Earth and World|language=en-US|access-date=2019-03-30|archive-date=30 March 2019|archive-url=https://web.archive.org/web/20190330124620/https://earthnworld.com/top-10-amazing-bioluminescent-animals-planet-earth/|url-status=live}}</ref> To add to the potential confusion, some organisms are both bioluminescent and fluorescent, like the sea pansy [[Renilla reniformis]], where bioluminescence serves as the light source for fluorescence.<ref>{{cite journal |last1=Ward |first1=William W. |last2=Cormier |first2=Milton J. |title=Energy Transfer Via Protein–Protein Interaction in Renilla Bioluminescence |journal=Photochemistry and Photobiology |date=1978 |volume=27 |issue=4 |pages=389–396 |doi=10.1111/j.1751-1097.1978.tb07621.x|s2cid=84887904 }}</ref>

==== Phosphorescence ====
[[Phosphorescence]] is similar to fluorescence in its requirement of light wavelengths as a provider of excitation energy. The difference here lies in the relative stability of the energized electron. Unlike with fluorescence, in phosphorescence the electron retains stability, emitting light that continues to "glow in the dark" even after the stimulating light source has been removed.<ref name="Fluorescence in marine organisms"/> For example, [[phosphorescence|glow-in-the-dark]] stickers are phosphorescent, but there are no truly ''biophosphorescent'' animals known.<ref>{{cite web|url=http://www.seasky.org/deep-sea/firefly-squid.html|title=Firefly Squid – Deep Sea Creatures on Sea and Sky|website=www.seasky.org|access-date=2019-03-30|archive-date=28 June 2019|archive-url=https://web.archive.org/web/20190628025334/http://www.seasky.org/deep-sea/firefly-squid.html|url-status=live}}</ref>

=== Mechanisms ===
==== Epidermal chromatophores ====
Pigment cells that exhibit fluorescence are called fluorescent chromatophores, and function somatically similar to regular [[chromatophore]]s. These cells are dendritic, and contain pigments called fluorosomes. These pigments contain fluorescent proteins which are activated by K+ (potassium) ions, and it is their movement, aggregation, and dispersion within the fluorescent chromatophore that cause directed fluorescence patterning.<ref name="wucherer" /><ref>
{{cite journal
 | pmid = 11041206
 | year = 2000
 | last1 = Fujii
 | first1 = R
 | title = The regulation of motile activity in fish chromatophores
 | journal = Pigment Cell Research
 | volume = 13
 | issue = 5
 | pages = 300–19
 | doi=10.1034/j.1600-0749.2000.130502.x
}}</ref> Fluorescent cells are innervated the same as other chromatophores, like melanophores, pigment cells that contain [[melanin]]. Short term fluorescent patterning and signaling is controlled by the nervous system.<ref name="wucherer" /> Fluorescent chromatophores can be found in the skin (e.g. in fish) just below the epidermis, amongst other chromatophores.

Epidermal fluorescent cells in fish also respond to hormonal stimuli by the α–MSH and MCH hormones much the same as melanophores. This suggests that fluorescent cells may have color changes throughout the day that coincide with their [[circadian rhythm]].<ref>{{Cite journal | doi = 10.1093/icb/13.3.885| title = Endocrine Regulation of Pigmentation in Fish| journal = Integrative and Comparative Biology| volume = 13| issue = 3| pages = 885–894| year = 1973| last1 = Abbott | first1 = F. S. | doi-access = free}}</ref> Fish may also be sensitive to [[cortisol]] induced [[stress response]]s to environmental stimuli, such as interaction with a predator or engaging in a mating ritual.<ref name="wucherer" />

=== Phylogenetics ===
==== Evolutionary origins ====
The incidence of fluorescence across the [[tree of life]] is widespread, and has been studied most extensively in cnidarians and fish. The phenomenon appears to have evolved multiple times in multiple [[Taxon|taxa]] such as in the anguilliformes (eels), gobioidei (gobies and cardinalfishes), and tetradontiformes (triggerfishes), along with the other taxa discussed later in the article. Fluorescence is highly genotypically and phenotypically variable even within ecosystems, in regards to the wavelengths emitted, the patterns displayed, and the intensity of the fluorescence. Generally, the species relying upon camouflage exhibit the greatest diversity in fluorescence, likely because camouflage may be one of the uses of fluorescence.<ref name="sparks">{{Cite journal | last1 = Sparks | first1 = J. S. | last2 = Schelly | first2 = R. C. | last3 = Smith | first3 = W. L. | last4 = Davis | first4 = M. P. | last5 = Tchernov | first5 = D. | last6 = Pieribone | first6 = V. A. | last7 = Gruber | first7 = D. F. | editor1-last = Fontaneto | editor1-first = Diego | title = The Covert World of Fish Biofluorescence: A Phylogenetically Widespread and Phenotypically Variable Phenomenon | doi = 10.1371/journal.pone.0083259 | journal = PLOS ONE| volume = 9 | issue = 1 | pages = e83259 | year = 2014 | pmid =  24421880| pmc = 3885428|bibcode = 2014PLoSO...983259S | doi-access = free }}</ref>

[[File:Observed occurrences of green and red biofluorescence in Actinopterygii - journal.pone.0083259.g002.png|thumb|alt=Observed occurrences of green and red biofluorescence in Actinopterygii|Fluorescence has multiple origins in the tree of life. This diagram displays the origins within actinopterygians (ray finned fish).]]

It is suspected by some scientists that [[Green fluorescent protein|GFPs]] and GFP-like proteins began as electron donors activated by light. These electrons were then used for reactions requiring light energy. Functions of fluorescent proteins, such as protection from the sun, conversion of light into different wavelengths, or for signaling are thought to have evolved secondarily.<ref name="Biology of underwater fluorescence">{{cite web|last1=Beyer|first1=Steffen|title=Biology of underwater fluorescence|url=https://translate.google.com/translate?sl=de&tl=en&prev=_t&hl=en&ie=UTF-8&u=http://www.fluopedia.org/publications/deutsch/biologie/|website=Fluopedia.org|access-date=19 January 2022|archive-date=30 July 2020|archive-url=https://web.archive.org/web/20200730070159/https://translate.google.com/translate?sl=de&tl=en&prev=_t&hl=en&ie=UTF-8&u=http%3A%2F%2Fwww.fluopedia.org%2Fpublications%2Fdeutsch%2Fbiologie%2F|url-status=live}}</ref>

==== Adaptive functions ====
Currently, relatively little is known about the functional significance of fluorescence and fluorescent proteins.<ref name="Biology of underwater fluorescence"/> However, it is suspected that fluorescence may serve important functions in signaling and communication, [[mating]], lures, [[camouflage]], [[UV protection]] and antioxidation, photoacclimation, [[dinoflagellate]] regulation, and in coral health.<ref name="HaddockDunn2015">{{cite journal|last1=Haddock|first1=S. H. D.|last2=Dunn|first2=C. W.|title=Fluorescent proteins function as a prey attractant: experimental evidence from the hydromedusa Olindias formosus and other marine organisms|journal=Biology Open|volume=4|issue=9|year=2015|pages=1094–1104|issn=2046-6390|doi=10.1242/bio.012138|pmid=26231627|pmc=4582119}}</ref>

=== Aquatic ===
Water absorbs light of long wavelengths, so less light from these wavelengths reflects back to reach the eye. Therefore, warm colors from the visual light spectrum appear less vibrant at increasing depths. Water scatters light of shorter wavelengths above violet, meaning cooler colors dominate the visual field in the [[photic zone]]. Light intensity decreases 10 fold with every 75 m of depth, so at depths of 75 m, light is 10% as intense as it is on the surface, and is only 1% as intense at 150 m as it is on the surface. Because the water filters out the wavelengths and intensity of water reaching certain depths, different proteins, because of the wavelengths and intensities of light they are capable of absorbing, are better suited to different depths. Theoretically, some fish eyes can detect light as deep as 1000 m. At these depths of the aphotic zone, the only sources of light are organisms themselves, giving off light through chemical reactions in a process called bioluminescence.

Fluorescence is simply defined as the absorption of electromagnetic radiation at one [[wavelength]] and its reemission at another, lower energy wavelength.<ref name="sparks" /> Thus any type of fluorescence depends on the presence of external sources of light. Biologically functional fluorescence is found in the photic zone, where there is not only enough light to cause fluorescence, but enough light for other organisms to detect it.<ref name="Mazel2017">{{cite journal|last1=Mazel|first1=Charles|title=Method for Determining the Contribution of Fluorescence to an Optical Signature, with Implications for Postulating a Visual Function|journal=Frontiers in Marine Science|volume=4|year=2017|page=266 |issn=2296-7745|doi=10.3389/fmars.2017.00266|doi-access=free|bibcode=2017FrMaS...4..266M }}</ref>
The visual field in the photic zone is naturally blue, so colors of fluorescence can be detected as bright reds, oranges, yellows, and greens. Green is the most commonly found color in the marine spectrum, yellow the second most, orange the third, and red is the rarest. Fluorescence can occur in organisms in the aphotic zone as a byproduct of that same organism's bioluminescence. Some fluorescence in the aphotic zone is merely a byproduct of the organism's tissue biochemistry and does not have a functional purpose. However, some cases of functional and adaptive significance of fluorescence in the aphotic zone of the deep ocean is an active area of research.<ref>{{cite web|last1=Matz|first1=M.|title=Fluorescence: The Secret Color of the Deep|url=http://oceanexplorer.noaa.gov/explorations/05deepscope/background/fluorescence/fluorescence.html|publisher=Office of Ocean Exploration and Research, U.S. National Oceanic and Atmospheric Administration|url-status=live|archive-url=https://web.archive.org/web/20141031213647/http://oceanexplorer.noaa.gov/explorations/05deepscope/background/fluorescence/fluorescence.html|archive-date=31 October 2014}}</ref>

==== Photic zone ====
{{main|Photic zone}}

===== Fish =====
[[File:Diversity of fluorescent patterns and colors in marine fishes - journal.pone.0083259.g001.png|thumb|Fluorescent marine fish]]
Bony fishes living in shallow water generally have good color vision due to their living in a colorful environment. Thus, in shallow-water fishes, red, orange, and green fluorescence most likely serves as a means of communication with [[Biological specificity|conspecifics]], especially given the great phenotypic variance of the phenomenon.<ref name="sparks"/>

Many fish that exhibit fluorescence, such as [[sharks]], [[lizardfish]], [[scorpionfish]], [[wrasses]], and [[flatfishes]], also possess yellow intraocular filters.<ref name="Heinermann">{{cite journal|last1=Heinermann|first1=P|title=Yellow intraocular filters in fishes|journal=Experimental Biology|date=2014-03-10|volume=43|issue=2|pages=127–147|pmid=6398222}}</ref> Yellow intraocular filters in the [[lens (anatomy)|lenses]] and [[cornea]] of certain fishes function as long-pass filters. These filters enable the species to visualize and potentially exploit fluorescence, in order to enhance visual contrast and patterns that are unseen to other fishes and predators that lack this visual specialization.<ref name="sparks"/> Fish that possess the necessary yellow intraocular filters for visualizing fluorescence potentially exploit a light signal from members of it. Fluorescent patterning was especially prominent in cryptically patterned fishes possessing complex camouflage. Many of these lineages also possess yellow long-pass intraocular filters that could enable visualization of such patterns.<ref name="Heinermann" />

Another adaptive use of fluorescence is to generate orange and red light from the ambient blue light of the [[photic zone]] to aid vision. Red light can only be seen across short distances due to attenuation of red light wavelengths by water.<ref name="michiels">{{Cite journal | doi = 10.1186/1472-6785-8-16| pmid = 18796150| pmc = 2567963| title = Red fluorescence in reef fish: A novel signalling mechanism?| journal = BMC Ecology| volume = 8| page = 16| year = 2008| last1 = Michiels | first1 = N. K. | last2 = Anthes | first2 = N. | last3 = Hart | first3 = N. S. | last4 = Herler | first4 = J. R. | last5 = Meixner | first5 = A. J. | last6 = Schleifenbaum | first6 = F. | last7 = Schulte | first7 = G. | last8 = Siebeck | first8 = U. E. | last9 = Sprenger | first9 = D. | last10 = Wucherer | first10 = M. F. | issue = 1| doi-access = free| bibcode = 2008BMCE....8...16M}}</ref> Many fish species that fluoresce are small, group-living, or benthic/aphotic, and have conspicuous patterning. This patterning is caused by fluorescent tissue and is visible to other members of the species, however the patterning is invisible at other visual spectra. These intraspecific fluorescent patterns also coincide with intra-species signaling. The patterns present in ocular rings to indicate directionality of an individual's gaze, and along fins to indicate directionality of an individual's movement.<ref name="michiels" /> Current research suspects that this red fluorescence is used for private communication between members of the same species.<ref name="wucherer">{{Cite journal | doi = 10.1371/journal.pone.0037913| pmid = 22701587| title = A Fluorescent Chromatophore Changes the Level of Fluorescence in a Reef Fish| journal = PLOS ONE| volume = 7| issue = 6| pages = e37913| year = 2012| last1 = Wucherer | first1 = M. F. | last2 = Michiels | first2 = N. K. |bibcode = 2012PLoSO...737913W | pmc=3368913| doi-access = free}}</ref><ref name="sparks" /><ref name="michiels" /> Due to the prominence of blue light at ocean depths, red light and light of longer wavelengths are muddled, and many predatory reef fish have little to no sensitivity for light at these wavelengths. Fish such as the fairy wrasse that have developed visual sensitivity to longer wavelengths are able to display red fluorescent signals that give a high contrast to the blue environment and are conspicuous to conspecifics in short ranges, yet are relatively invisible to other common fish that have reduced sensitivities to long wavelengths. Thus, fluorescence can be used as adaptive signaling and intra-species communication in reef fish.<ref name="michiels" /><ref name="gerlach">
{{cite journal
 | pmid = 24870049
 | pmc = 4071555
 | year = 2014
 | last1 = Gerlach
 | first1 = T
 | title = Fairy wrasses perceive and respond to their deep red fluorescent coloration
 | journal = Proceedings of the Royal Society B: Biological Sciences
 | volume = 281
 | issue = 1787
 | page = 20140787
 | last2 = Sprenger
 | first2 = D
 | last3 = Michiels
 | first3 = N. K.
 | doi = 10.1098/rspb.2014.0787
}}</ref>

Additionally, it is suggested that fluorescent [[tissue (biology)|tissues]] that surround an organism's eyes are used to convert blue light from the photic zone or green bioluminescence in the aphotic zone into red light to aid vision.<ref name="michiels" />

===== Sharks =====
A new [[fluorophore]] was described in two species of sharks, wherein it was due to an undescribed group of brominated tryptophane-kynurenine small molecule metabolites.<ref>{{Cite journal|last1=Park|first1=Hyun Bong|last2=Lam|first2=Yick Chong|last3=Gaffney|first3=Jean P.|last4=Weaver|first4=James C.|last5=Krivoshik|first5=Sara Rose|last6=Hamchand|first6=Randy|last7=Pieribone|first7=Vincent|last8=Gruber|first8=David F.|last9=Crawford|first9=Jason M.|date=2019-09-27|title=Bright Green Biofluorescence in Sharks Derives from Bromo-Kynurenine Metabolism|url= |journal=iScience|language=en|volume=19|pages=1291–1336|doi=10.1016/j.isci.2019.07.019|issn=2589-0042|pmid=31402257|pmc=6831821|bibcode=2019iSci...19.1291P}}</ref>

===== Coral =====
Fluorescence serves a wide variety of functions in coral. Fluorescent proteins in corals may contribute to photosynthesis by converting otherwise unusable wavelengths of light into ones for which the coral's symbiotic algae are able to conduct [[photosynthesis]].<ref>{{Cite journal | doi = 10.1038/35048564 | pmid = 11130722 | title = Fluorescent pigments in corals are photoprotective | year = 2000 | last1 = Salih | first1 = A. | journal = Nature | volume = 408 | issue = 6814 | pages = 850–3 | last2 = Larkum | first2 = A. | last3 = Cox | first3 = G. | last4 = Kühl | first4 = M. | last5 = Hoegh-Guldberg | first5 = O. | url = https://www.researchgate.net/publication/12197663 | bibcode = 2000Natur.408..850S | s2cid = 4300578 | url-status = live | archive-url = https://web.archive.org/web/20151222103614/https://www.researchgate.net/publication/12197663_Fluorescent_Pigments_in_Corals_are_Photoprotective | archive-date = 22 December 2015}}</ref> Also, the proteins may fluctuate in number as more or less light becomes available as a means of photoacclimation.<ref>{{Cite journal | doi = 10.1242/jeb.040881| title = Green fluorescent protein regulation in the coral Acropora yongei during photoacclimation| journal = Journal of Experimental Biology| volume = 213| issue = 21| pages = 3644–3655| year = 2010| last1 = Roth | first1 = M. S.| last2 = Latz | first2 = M. I.| last3 = Goericke | first3 = R.| last4 = Deheyn | first4 = D. D. | pmid=20952612| doi-access = free| bibcode = 2010JExpB.213.3644R}}</ref> Similarly, these fluorescent proteins may possess antioxidant capacities to eliminate oxygen radicals produced by photosynthesis.<ref>{{Cite journal | doi = 10.1016/j.bbagen.2006.08.014| title = Quenching of superoxide radicals by green fluorescent protein| journal = Biochimica et Biophysica Acta (BBA) - General Subjects| volume = 1760| issue = 11| pages = 1690–1695| year = 2006| last1 = Bou-Abdallah | first1 = F. | last2 = Chasteen | first2 = N. D. | last3 = Lesser | first3 = M. P. | pmid=17023114 | pmc=1764454}}</ref> Finally, through modulating photosynthesis, the fluorescent proteins may also serve as a means of regulating the activity of the coral's photosynthetic algal symbionts.<ref>{{Cite journal | doi = 10.1007/s00239-005-0129-9| title = Adaptive Evolution of Multicolored Fluorescent Proteins in Reef-Building Corals| journal = Journal of Molecular Evolution| volume = 62| issue = 3| pages = 332–339| year = 2006| last1 = Field | first1 = S. F. | last2 = Bulina | first2 = M. Y. | last3 = Kelmanson | first3 = I. V. | last4 = Bielawski | first4 = J. P. | last5 = Matz | first5 = M. V. | pmid=16474984| bibcode = 2006JMolE..62..332F| s2cid = 12081922}}</ref>

===== Cephalopods =====
{{main|Cephalopods}}
''Alloteuthis subulata'' and ''Loligo vulgaris'', two types of nearly transparent squid, have fluorescent spots above their eyes. These spots reflect incident light, which may serve as a means of camouflage, but also for signaling to other squids for schooling purposes.<ref>
{{cite journal
 |pmid        = 11441052
 |url         = http://jeb.biologists.org/content/204/12/2103.short
 |year        = 2001
 |last1     = Mäthger
 |first1      = L. M.
 |title       = Reflective properties of iridophores and fluorescent 'eyespots' in the loliginid squid ''Alloteuthis subulata'' and ''Loligo vulgaris''
 |journal     = The Journal of Experimental Biology
 |volume      = 204
 |issue       = Pt 12
 |pages       = 2103–18
 |last2       = Denton
 |first2      = E. J.
 |doi = 10.1242/jeb.204.12.2103
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 |author-link2 = Eric James Denton
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 |archive-url  = https://web.archive.org/web/20160304110727/http://jeb.biologists.org/content/204/12/2103.short
 |archive-date = 4 March 2016
}}</ref>

===== Jellyfish =====
[[File:Crystal Jelly ("Aequorea Victoria"), Monterey Bay Aquarium, Monterey, California, USA.jpg|thumb|''Aequoria victoria'', biofluorescent jellyfish known for GFP]]
Another, well-studied example of fluorescence in the ocean is the [[hydrozoan]] ''[[Aequorea victoria]]''. This jellyfish lives in the photic zone off the west coast of North America and was identified as a carrier of [[green fluorescent protein]] (GFP) by [[Osamu Shimomura]]. The gene for these green fluorescent proteins has been isolated and is scientifically significant because it is widely used in genetic studies to indicate the expression of other genes.<ref>{{Cite journal | doi = 10.1146/annurev.biochem.67.1.509| title = The Green Fluorescent Protein| journal = Annual Review of Biochemistry| volume = 67| pages = 509–544| year = 1998| last1 = Tsien | first1 = R. Y.| s2cid = 8138960| pmid=9759496}}</ref>

===== Mantis shrimp =====
Several species of [[mantis shrimp]], which are stomatopod [[crustaceans]], including ''Lysiosquillina glabriuscula'', have yellow fluorescent markings along their antennal scales and [[carapace]] (shell) that males present during threat displays to predators and other males. The display involves raising the head and thorax, spreading the striking appendages and other maxillipeds, and extending the prominent, oval antennal scales laterally, which makes the animal appear larger and accentuates its yellow fluorescent markings. Furthermore, as depth increases, mantis shrimp fluorescence accounts for a greater part of the visible light available. During mating rituals, mantis shrimp actively fluoresce, and the wavelength of this fluorescence matches the wavelengths detected by their eye pigments.<ref>{{Cite journal | doi = 10.1126/science.1089803| title = Fluorescent Enhancement of Signaling in a Mantis Shrimp| journal = Science| volume = 303| issue = 5654| page = 51| year = 2004| last1 = Mazel | first1 = C. H.| s2cid = 35009047| pmid=14615546| doi-access = free}}</ref>

==== Aphotic zone ====
{{main|Aphotic zone}}

===== Siphonophores =====
''[[Siphonophorae]]'' is an order of marine animals from the phylum [[Hydrozoa]] that consist of a specialized [[jellyfish|medusoid]] and [[polyp (zoology)|polyp]] [[zooid]]. Some siphonophores, including the genus Erenna that live in the aphotic zone between depths of 1600 m and 2300 m, exhibit yellow to red fluorescence in the [[photophores]] of their tentacle-like [[tentilla]]. This fluorescence occurs as a by-product of bioluminescence from these same photophores. The siphonophores exhibit the fluorescence in a flicking pattern that is used as a lure to attract prey.<ref>
{{cite journal
 | doi = 10.1016/j.bbagen.2006.08.014
 | title = Quenching of superoxide radicals by green fluorescent protein
 | journal = Biochimica et Biophysica Acta (BBA) - General Subjects
 | volume = 1760
 | issue = 11
 | pages = 1690–1695
 | year = 2006
 | last1 = Bou-Abdallah | first1 = F.
 | last2 = Chasteen | first2 = N. D.
 | last3 = Lesser | first3 = M. P.
 | pmid=17023114
 | pmc=1764454
}}</ref>

===== Dragonfish =====
The predatory deep-sea [[Barbeled dragonfish|dragonfish]] ''Malacosteus niger'', the closely related genus ''[[Aristostomias]]'' and the species ''[[Pachystomias microdon]]'' use fluorescent red accessory pigments to convert the blue light emitted from their own bioluminescence to red light from suborbital [[photophores]]. This red luminescence is invisible to other animals, which allows these dragonfish extra light at dark ocean depths without attracting or signaling predators.<ref>{{Cite journal | doi = 10.1038/30871|title=Dragon fish see using chlorophyll|bibcode=1998Natur.393..423D| year = 1998| last1 = Douglas | first1 = R. H.| journal = Nature| volume = 393| issue = 6684| pages = 423–424| last2 = Partridge | first2 = J. C.| last3 = Dulai | first3 = K.| last4 = Hunt | first4 = D.| last5 = Mullineaux | first5 = C. W.| last6 = Tauber | first6 = A. Y.| last7 = Hynninen | first7 = P. H.|s2cid=4416089}}</ref>

=== Terrestrial ===
==== Amphibians ====
[[File:Hypsiboas punctatus fluorescente.jpg|thumb|Fluorescent [[polka-dot tree frog]] under UV-light]]

Fluorescence is widespread among [[amphibian]]s and has been documented in several families of [[frog]]s, [[salamander]]s and [[caecilian]]s, but the extent of it varies greatly.<ref name=Lamb2020>{{cite journal | author1=Lamb, J.Y. | author2=M.P. Davis | year=2020 | title=Salamanders and other amphibians are aglow with biofluorescence | journal=Scientific Reports | volume=10 | issue=1 | page=2821 | doi=10.1038/s41598-020-59528-9 | pmid=32108141 | pmc=7046780 | bibcode=2020NatSR..10.2821L }}</ref>

The [[polka-dot tree frog]] (''Hypsiboas punctatus''), widely found in South America, was unintentionally discovered to be the first fluorescent amphibian in 2017. The fluorescence was traced to a new compound found in the [[lymph]] and skin glands.<ref>{{cite news |last=Wong |first=Sam |date=13 March 2017 |title=Luminous frog is the first known naturally fluorescent amphibian |url=https://www.newscientist.com/article/2124466-luminous-frog-is-the-first-known-naturally-fluorescent-amphibian/ |access-date=2017-03-22 |url-status=live |archive-url=https://web.archive.org/web/20170320143233/https://www.newscientist.com/article/2124466-luminous-frog-is-the-first-known-naturally-fluorescent-amphibian/ |archive-date=20 March 2017}}</ref> The main fluorescent compound is Hyloin-L1 and it gives a blue-green glow when exposed to violet or [[ultraviolet light]]. The scientists behind the discovery suggested that the fluorescence can be used for communication. They speculated that fluorescence possibly is relatively widespread among frogs.<ref>{{cite news |last=King |first=Anthony |date=13 March 2017 |title=Fluorescent frog first down to new molecule |url=https://www.chemistryworld.com/news/fluorescent-frog-first-down-to-new-molecule-/2500541.article |access-date=2017-03-22 |url-status=live |archive-url=https://web.archive.org/web/20170322191916/https://www.chemistryworld.com/news/fluorescent-frog-first-down-to-new-molecule-/2500541.article |archive-date=22 March 2017}}</ref> Only a few months later, fluorescence was discovered in the closely related ''[[Hypsiboas atlanticus]]''. Because it is linked to secretions from skin glands, they can also leave fluorescent markings on surfaces where they have been.<ref name=Taboada2017>{{cite journal | author1=Taboada, C. | author2=A.E. Brunetti | author3=C. Alexandre | author4=M.G. Lagorio | author5=J. Faivovich | year=2017 | title=Fluorescent Frogs: A Herpetological Perspective | journal=South American Journal of Herpetology | volume=12 | issue=1 | pages=1–13 | doi=10.2994/SAJH-D-17-00029.1 | s2cid=89815080 | hdl=11336/48638 | hdl-access=free }}</ref>

In 2019, two other frogs, the tiny [[pumpkin toadlet]] (''Brachycephalus ephippium'') and [[red pumpkin toadlet]] (''B. pitanga'') of southeastern Brazil, were found to have naturally fluorescent skeletons, which are visible through their skin when exposed to ultraviolet light.<ref name=Goutte2019>{{cite journal | author1=Sandra Goutte | author2=Matthew J. Mason | author3=Marta M. Antoniazzi | author4=Carlos Jared | author5=Didier Merle | author6=Lilian Cazes | author7=Luís Felipe Toledo | author8=Hanane el-Hafci | author9=Stéphane Pallu | author10=Hugues Portier | author11=Stefan Schramm | author12=Pierre Gueriau | author13=Mathieu Thoury | year=2019 | title=Intense bone fluorescence reveals hidden patterns in pumpkin toadlets | journal=Scientific Reports | volume=9 | issue=1 | page=5388 | doi=10.1038/s41598-019-41959-8 | pmid=30926879 | pmc=6441030 | bibcode=2019NatSR...9.5388G }}</ref><ref name=Fox2019>{{cite web | author=Fox, A. | title=Scientists discover a frog with glowing bones | url=https://www.science.org/content/article/scientists-discover-frog-glowing-bones | date=2 April 2019 | website=ScienceMag | access-date=9 February 2020 | archive-date=8 March 2020 | archive-url=https://web.archive.org/web/20200308114612/https://www.sciencemag.org/news/2019/04/scientists-discover-frog-glowing-bones | url-status=live }}</ref> It was initially speculated that the fluorescence supplemented their already [[aposematic]] colours (they are toxic) or that it was related to [[mate choice]] ([[species recognition]] or determining fitness of a potential partner),<ref name=Goutte2019/> but later studies indicate that the former explanation is unlikely, as predation attempts on the toadlets appear to be unaffected by the presence/absence of fluorescence.<ref name=Reboucas2019>{{cite journal | author1=Rebouças, R. | author2=A.B. Carollo | author3=M.d.O. Freitas | author4=C. Lambertini | author5=R.M. Nogueira dos Santos | author6=L.F. Toledo | year=2019 | title=  Conservation Status of Brachycephalus Toadlets (Anura: Brachycephalidae) from the Brazilian Atlantic Rainforest| journal= Diversity| volume=55 | issue=1 | pages=39–47 | doi=10.3390/d11090150 | doi-access=free | bibcode=2019Diver..11..150B }}</ref>

In 2020 it was confirmed that green or yellow fluorescence is widespread not only in adult frogs that are exposed to blue or ultraviolet light, but also among [[tadpole]]s, salamanders and caecilians. The extent varies greatly depending on species; in some it is highly distinct and in others it is barely noticeable. It can be based on their skin pigmentation, their mucus or their bones.<ref name=Lamb2020/>

==== Butterflies ====
[[swallowtail butterfly|Swallowtail]] (''Papilio'') butterflies have complex systems for emitting fluorescent light. Their wings contain pigment-infused crystals that provide directed fluorescent light. These crystals function to produce fluorescent light best when they absorb [[radiance]] from sky-blue light (wavelength about 420&nbsp;nm). The wavelengths of light that the butterflies see the best correspond to the absorbance of the crystals in the butterfly's wings. This likely functions to enhance the capacity for signaling.<ref>
{{cite journal
 | pmid = 16293753
 | year = 2005
 | last1 = Vukusic
 | first1 = P
 | title = Directionally controlled fluorescence emission in butterflies
 | journal = Science
 | volume = 310
 | issue = 5751
 | page = 1151
 | last2 = Hooper
 | first2 = I
 | s2cid = 43857104
 | doi = 10.1126/science.1116612
}}</ref>

==== Parrots ====
[[Parrots]] have fluorescent [[plumage]] that may be used in mate signaling. A study using mate-choice experiments on [[budgerigars]] (''Melopsittacus undulates'') found compelling support for fluorescent sexual signaling, with both males and females significantly preferring birds with the fluorescent experimental stimulus. This study suggests that the fluorescent plumage of parrots is not simply a by-product of [[pigmentation]], but instead an adapted sexual signal. Considering the intricacies of the pathways that produce fluorescent pigments, there may be significant costs involved. Therefore, individuals exhibiting strong fluorescence may be honest indicators of high individual quality, since they can deal with the associated costs.<ref>{{Cite journal| doi = 10.1126/science.295.5552.92| pmid = 11778040| title = Fluorescent Signaling in Parrots| journal = Science| volume = 295| issue = 5552| page = 92| year = 2002| last1 = Arnold| first1 = K. E.| citeseerx = 10.1.1.599.1127}}</ref>

==== Arachnids ====
[[File:Sorpion Under Blacklight edit.jpg|thumb|Fluorescing scorpion]]
Spiders fluoresce under UV light and possess a huge diversity of fluorophores. Andrews, Reed, & Masta noted that spiders are the only known group in which fluorescence is "taxonomically widespread, variably expressed, evolutionarily labile, and probably under selection and potentially of ecological importance for intraspecific and interspecific signaling".<ref name=Andrews-Reed-Masta-2007/> They showed that fluorescence evolved multiple times across spider taxa, with novel fluorophores evolving during spider diversification.

In some spiders, ultraviolet cues are important for predator–prey interactions, intraspecific communication, and camouflage-matching with fluorescent flowers. Differing ecological contexts could favor inhibition or enhancement of fluorescence expression, depending upon whether fluorescence helps spiders be cryptic or makes them more conspicuous to predators. Therefore, natural selection could be acting on expression of fluorescence across spider species.<ref name=Andrews-Reed-Masta-2007>
{{cite journal
 | last1 = Andrews | first1 = K.
 | last2 = Reed    | first2 = S.M.
 | last3 = Masta   | first3 = S.E.
 | year = 2007
 | title = Spiders fluoresce variably across many taxa
 | journal = Biology Letters
 | volume = 3  | issue = 3  | pages = 265–267
 | doi = 10.1098/rsbl.2007.0016
 | pmid = 17412670  | pmc = 2104643
}}</ref>

Scorpions are also fluorescent, in their case due to the presence of [[beta-carboline]] in their cuticles.<ref name=Stachel-Stockwell-vanVranken-1999>
{{cite journal
 | last1 = Stachel     | first1 = S.J.
 | last2 = Stockwell   | first2 = S.A.
 | last3 = van Vranken | first3 = D.L.
 | year = 1999
 | title = The fluorescence of scorpions and cataractogenesis
 | journal = Chemistry & Biology
 | volume = 6  | issue = 8  | pages = 531–539
 | doi = 10.1016/S1074-5521(99)80085-4
 | doi-access = free   | pmid=10421760
}}
</ref>

==== Platypus ====
In 2020 fluorescence was reported for several [[platypus]] specimens.<ref>
{{cite journal
 | last = Spaeth  | first = P.
 | year = 2020
 | title = Biofluorescence in the platypus (Ornithorhynchus anatinus)
 | journal = Mammalia
 | volume = 85  | issue = 2  | pages = 179–181
 | doi = 10.1515/mammalia-2020-0027
 | doi-access = free
}}</ref>

==== Plants ====
Many plants are fluorescent due to the presence of [[chlorophyll]], which is probably the most widely distributed fluorescent molecule, producing red emission under a range of excitation wavelengths.<ref>{{Cite book|url=https://books.google.com/books?id=x2PZRC6Zd5sC&q=Chlorophyll+fluoresces+a+weak+red+under+ultraviolet+light.&pg=PA12|title=Photobiology of Higher Plants|last=McDonald|first=Maurice S.|date=2003-06-02|publisher=John Wiley & Sons|isbn=9780470855232|language=en|url-status=live|archive-url=https://web.archive.org/web/20171221200631/https://books.google.com/books?id=x2PZRC6Zd5sC&pg=PA12&dq=Chlorophyll+fluoresces+a+weak+red+under+ultraviolet+light.&hl=en&sa=X&ved=0ahUKEwiRlYCz85vYAhWJgVQKHZhsDrYQ6AEIODAD#v=onepage&q=Chlorophyll%20fluoresces%20a%20weak%20red%20under%20ultraviolet%20light.&f=false|archive-date=21 December 2017}}</ref> This attribute of chlorophyll is commonly used by ecologists to measure photosynthetic efficiency.<ref>{{Cite web|url=https://climexhandbook.w.uib.no/2019/11/03/chlorophyll-fluorescence/|title=5.1 Chlorophyll fluorescence – ClimEx Handbook|language=en-US|access-date=2020-01-14|archive-date=14 January 2020|archive-url=https://web.archive.org/web/20200114153538/https://climexhandbook.w.uib.no/2019/11/03/chlorophyll-fluorescence/|url-status=live}}</ref>

The ''Mirabilis jalapa'' flower contains violet, fluorescent betacyanins and yellow, fluorescent betaxanthins. Under white light, parts of the flower containing only betaxanthins appear yellow, but in areas where both betaxanthins and betacyanins are present, the visible fluorescence of the flower is faded due to internal light-filtering mechanisms. Fluorescence was previously suggested to play a role in [[pollinator]] attraction, however, it was later found that the visual signal by fluorescence is negligible compared to the visual signal of light reflected by the flower.<ref>{{Cite journal | doi = 10.1007/s00114-010-0709-4| title = Is the flower fluorescence relevant in biocommunication?| journal = Naturwissenschaften| volume = 97| issue = 10| pages = 915–924| year = 2010| last1 = Iriel | first1 = A. A. | last2 = Lagorio | first2 = M. A. G. |bibcode = 2010NW.....97..915I | pmid=20811871| s2cid = 43503960}}</ref>

=== Abiotic ===
==== Gemology, mineralogy and geology ====
[[File:Aragonit - Fluorescence.gif|thumb|left|Fluorescence of [[aragonite]]]]
[[File:Rough diamonds - necklace in UV and normal light B - composite.jpg|thumb|left|Necklace of rough diamonds under [[Blacklight|UV light]] (top) and normal light (bottom)]]
In addition to the eponymous [[fluorspar]],<ref>Raman, C.V., (1962). [https://www.currentscience.ac.in/Volumes/31/09/0361.pdf "The luminescence of fluorspar"], Curr. Sci., 31, 361–365</ref> many
[[gemstone]]s and [[mineral]]s may have a distinctive fluorescence or may fluoresce differently under short-wave ultraviolet, long-wave ultraviolet, visible light, or [[X-ray]]s.

Many types of [[calcite]] and [[amber]] will fluoresce under shortwave UV, longwave UV and visible light. [[Ruby|Rubies]], [[emerald]]s, and [[diamond]]s exhibit red fluorescence under long-wave UV, blue and sometimes green light; diamonds also emit light under [[X-ray]] radiation.

Fluorescence in minerals is caused by a wide range of [[Activator (phosphor)|activators]]. In some cases, the concentration of the activator must be restricted to below a certain level, to prevent quenching of the fluorescent emission. Furthermore, the mineral must be free of impurities such as [[iron]] or [[copper]], to prevent quenching of possible fluorescence. Divalent [[manganese]], in concentrations of up to several percent, is responsible for the red or orange fluorescence of [[calcite]], the green fluorescence of [[willemite]], the yellow fluorescence of [[esperite]], and the orange fluorescence of [[wollastonite]] and [[clinohedrite]]. Hexavalent [[uranium]], in the form of the [[uranyl cation]] ({{chem|UO|2|2+}}), fluoresces at all concentrations in a yellow green, and is the cause of fluorescence of minerals such as [[autunite]] or [[andersonite]], and, at low concentration, is the cause of the fluorescence of such materials as some samples of [[hyalite]] [[opal]]. Trivalent [[chromium]] at low concentration is the source of the red fluorescence of [[ruby]]. Divalent [[europium]] is the source of the blue fluorescence, when seen in the mineral [[fluorite]]. Trivalent [[lanthanide]]s such as [[terbium]] and [[dysprosium]] are the principal activators of the creamy yellow fluorescence exhibited by the [[yttrofluorite]] variety of the mineral fluorite, and contribute to the orange fluorescence of [[zircon]]. [[Powellite]] ([[calcium molybdate]]) and [[scheelite]] (calcium tungstate) fluoresce intrinsically in yellow and blue, respectively. When present together in [[solid solution]], energy is transferred from the higher-energy [[tungsten]] to the lower-energy [[molybdenum]], such that fairly low levels of [[molybdenum]] are sufficient to cause a yellow emission for [[scheelite]], instead of blue. Low-iron [[sphalerite]] (zinc sulfide), fluoresces and phosphoresces in a range of colors, influenced by the presence of various trace impurities.

Crude oil ([[petroleum]]) fluoresces in a range of colors, from dull-brown for heavy oils and tars through to bright-yellowish and bluish-white for very light oils and condensates. This phenomenon is used in [[oil exploration]] drilling to identify very small amounts of oil in drill cuttings and core samples.

[[Humic acid]]s and [[fulvic acid]]s produced by the degradation of [[organic matter]] in soils ([[humus]]) may also fluoresce because of the presence of aromatic cycles in their complex [[molecular structure]]s.<ref name="Mobed_1966">{{Cite journal| doi = 10.1021/es960132l| issn = 0013-936X| volume = 30| issue = 10| pages = 3061–3065| last1 = Mobed| first1 = Jarafshan J.| last2 = Hemmingsen| first2 = Sherry L.| last3 = Autry| first3 = Jennifer L.| last4 = McGown| first4 = Linda B.| title = Fluorescence characterization of IHSS humic substances: Total luminescence spectra with absorbance correction| journal = Environmental Science & Technology| accessdate = 2021-08-29| date = 1996-09-01| bibcode = 1996EnST...30.3061M| url = https://doi.org/10.1021/es960132l| archive-date = 4 May 2022| archive-url = https://web.archive.org/web/20220504144922/https://pubs.acs.org/doi/10.1021/es960132l| url-status = live}}</ref> Humic substances dissolved in [[groundwater]] can be detected and characterized by [[spectrofluorimetry]].<ref name="Milori_2002">{{Cite journal| issn = 0038-075X| volume = 167| issue = 11| pages = 739–749| last1 = Milori| first1 = Débora MBP| last2 = Martin-Neto| first2 = Ladislau| last3 = Bayer| first3 = Cimélio| last4 = Mielniczuk| first4 = João| last5 = Bagnato| first5 = Vanderlei S| title = Humification degree of soil humic acids determined by fluorescence spectroscopy| journal = Soil Science| date = 2002| doi = 10.1097/00010694-200211000-00004| bibcode = 2002SoilS.167..739M| s2cid = 98552138}}</ref>
<ref name="Richard_2004">{{Cite journal| issn = 0013-936X| volume = 38| issue = 7| pages = 2052–2057| last1 = Richard| first1 = C| last2 = Trubetskaya| first2 = O| last3 = Trubetskoj| first3 = O| last4 = Reznikova| first4 = O| last5 = Afanas' Eva| first5 = G| last6 = Aguer| first6 = J-P| last7 = Guyot| first7 = G| title = Key role of the low molecular size fraction of soil humic acids for fluorescence and photoinductive activity| journal = Environmental Science & Technology| date = 2004| doi = 10.1021/es030049f| pmid = 15112806| bibcode = 2004EnST...38.2052R}}</ref>
<ref name="Sierra_2005">{{Cite journal| issn = 0045-6535| volume = 58| issue = 6| pages = 715–733| last1 = Sierra| first1 = MMD| last2 = Giovanela| first2 = M| last3 = Parlanti| first3 = E| last4 = Soriano-Sierra| first4 = EJ| title = Fluorescence fingerprint of fulvic and humic acids from varied origins as viewed by single-scan and excitation/emission matrix techniques| journal = Chemosphere| date = 2005| doi = 10.1016/j.chemosphere.2004.09.038| pmid = 15621185| bibcode = 2005Chmsp..58..715S}}</ref>

==== Organic liquids ====
[[File:Fluorescence in beer @ 450nm illumination.jpg|thumb|Organic molecules found naturally in beer, such as [[tryptophan]], [[tyrosine]], and [[phenylalanine]], fluoresce in green, ranging from 500 nm (light blue) to 600 nm (amber yellow) when illuminated with 450 nm (deep blue) laser light.<ref>{{cite journal | url=https://link.springer.com/article/10.1007/s10895-019-02421-0 | doi=10.1007/s10895-019-02421-0 | title=The Parallel Factor Analysis of Beer Fluorescence | date=2019 | last1=Dramićanin | first1=Tatjana | last2=Zeković | first2=Ivana | last3=Periša | first3=Jovana | last4=Dramićanin | first4=Miroslav D. | journal=Journal of Fluorescence | volume=29 | issue=5 | pages=1103–1111 | pmid=31396828 }}</ref>]]
Organic (carbon based) solutions such [[anthracene]] or [[stilbene]], dissolved in [[benzene]] or [[toluene]], fluoresce with [[ultraviolet]] or [[gamma ray]] [[irradiation]]. The decay times of this fluorescence are on the order of nanoseconds, since the duration of the light depends on the lifetime of the excited states of the fluorescent material, in this case anthracene or stilbene.<ref>{{Cite journal |doi = 10.1088/0370-1328/79/3/306|title = The Fluorescence and Scintillation Decay Times of Crystalline Anthracene|journal = Proceedings of the Physical Society|volume = 79|issue = 3|pages = 494–496|year = 1962|last1 = Birks|first1 = J. B.|s2cid = 17394465|bibcode = 1962PPS....79..494B}}</ref>

[[Scintillation (physics)|Scintillation]] is defined a flash of light produced in a transparent material by the passage of a particle (an electron, an alpha particle, an ion, or a high-energy photon). Stilbene and derivatives are used in [[scintillation counter]]s to detect such particles. Stilbene is also one of the [[gain medium]]s used in [[dye lasers]].

==== Atmosphere ====
Fluorescence is observed in the atmosphere when the air is under energetic electron bombardment. In cases such as the natural [[aurora]], high-altitude nuclear explosions, and rocket-borne electron gun experiments, the molecules and ions formed have a fluorescent response to light.<ref name=gilmore1992>
{{Cite journal| doi = 10.1063/1.555910| title = Franck–Condon Factors, r-Centroids, Electronic Transition Moments, and Einstein Coefficients for Many Nitrogen and Oxygen Band Systems| journal = Journal of Physical and Chemical Reference Data| volume = 21| issue = 5| page = 1005| year = 1992| last1 = Gilmore| first1 = F. R.| last2 = Laher| first2 = R. R.| last3 = Espy| first3 = P. J.| bibcode = 1992JPCRD..21.1005G| url = https://apps.dtic.mil/sti/citations/ADA246065| url-status = live| archive-url = https://web.archive.org/web/20170709141516/http://www.dtic.mil/docs/citations/ADA246065| archive-date = 9 July 2017}}</ref>

==== Common materials that fluoresce ====
* [[Vitamin B2]] fluoresces green, with an emission centered ~525 nm.
* [[Tonic water]] fluoresces blue due to the presence of [[quinine]].
* [[Highlighter]] ink is often fluorescent due to the presence of [[pyranine]].
* [[Banknote]]s, [[postage stamp]]s and [[credit card]]s often have fluorescent security features.