Editing Fluorescence (section)

=== 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
 |bibcode = 2001JExpB.204.2103M
 |author-link2 = Eric James Denton
 |url-status     = live
 |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>