Editing Coral (section)

== Systematics ==
{{External links|section|date=August 2023}}
The delineation of coral species is challenging as hypotheses based on morphological traits contradict hypotheses formed via molecular tree-based processes.<ref name=":1">{{Cite journal |last1=Ramírez-Portilla |first1=Catalina |last2=Baird |first2=Andrew H |last3=Cowman |first3=Peter F |last4=Quattrini |first4=Andrea M |last5=Harii |first5=Saki |last6=Sinniger |first6=Frederic |last7=Flot |first7=Jean-François |date=2022-03-01 |title=Solving the Coral Species Delimitation Conundrum |journal=Systematic Biology |volume=71 |issue=2 |pages=461–475 |doi=10.1093/sysbio/syab077 |pmid=34542634 |issn=1063-5157|doi-access=free }}</ref> As of 2020, there are 2175 identified separate coral species, 237 of which are currently endangered,<ref>{{Cite journal |last1=Ritchie |first1=Hannah |author1-link=Hannah Ritchie |last2=Roser |first2=Max |author2-link=Max Roser |date=2021-04-15 |title=Biodiversity |url=https://ourworldindata.org/coral-reefs |journal=Our World in Data}}</ref> making distinguishing corals to be the utmost of importance in efforts to curb extinction.<ref name=":1" />&nbsp;[[Adaptation]] and delineation continues to occur in species of coral<ref>{{Cite journal |last1=Hume |first1=Benjamin C. C. |last2=D'Angelo |first2=Cecilia |last3=Burt |first3=John A. |last4=Wiedenmann |first4=Jörg |date=2018 |title=Fine-Scale Biogeographical Boundary Delineation and Sub-population Resolution in the Symbiodinium thermophilum Coral Symbiont Group From the Persian/Arabian Gulf and Gulf of Oman |journal=Frontiers in Marine Science |volume=5 |doi=10.3389/fmars.2018.00138 |issn=2296-7745|doi-access=free |hdl=10754/627647 |hdl-access=free }}</ref> in order to combat the dangers posed by the climate crisis. Corals are [[Colony (biology)|colonial modular organisms]] formed by [[Asexual reproduction|asexually]] produced and genetically identical modules called polyps. Polyps are connected by living tissue to produce the full organism.<ref name=":2">{{Cite journal |last1=Hemond |first1=Elizabeth M |last2=Kaluziak |first2=Stefan T |last3=Vollmer |first3=Steven V |date=2014-12-17 |title=The genetics of colony form and function in Caribbean Acropora corals |journal=BMC Genomics |volume=15 |pages=1133 |doi=10.1186/1471-2164-15-1133 |issn=1471-2164 |pmc=4320547 |pmid=25519925 |doi-access=free }}</ref>&nbsp;The living tissue allows for inter module communication (interaction between each polyp),<ref name=":2" /> which appears in colony [[Morphology (biology)|morphologies]] produced by corals, and is one of the main identifying characteristics for&nbsp;a species of coral.<ref name=":2" />

There are two main classifications for corals: hard coral (scleractinian and stony coral)<ref name=":3">{{Cite web |last=US Department of Commerce |first=National Oceanic and Atmospheric Administration |title=NOAA's Coral Reef Conservation Program (CRCP) – Coral Facts |url=https://coralreef.noaa.gov/education/ |access-date=2022-04-26 |website=coralreef.noaa.gov |language=EN-US}}</ref> which form reefs by a calcium carbonate base, with polyps that bear six stiff tentacles,<ref name=":4">{{Cite web |title=Soft Corals: They Look Like Plants But Are Actually Animals |url=https://www.thoughtco.com/soft-corals-octocorals-2291391 |access-date=2022-04-26 |website=ThoughtCo |language=en}}</ref> and soft coral (Alcyonacea and ahermatypic coral)<ref name=":3" /> which are pliable and formed by a colony of polyps with eight feather-like tentacles.<ref name=":4" />&nbsp;These two classifications arose from [https://www.ncbi.nlm.nih.gov/books/NBK10061/ differentiation in gene expressions] in their branch tips<ref name=":2" /> and bases that arose through developmental signaling pathways such as [[Hox gene|Hox]], [[Hedgehog signaling pathway|Hedgehog]], [[Wnt signaling pathway|Wnt]], [https://pubmed.ncbi.nlm.nih.gov/25401122/ BMP] etc.

Scientists typically select ''Acropora'' as research models since they are the most diverse genus of hard coral, having over 120 species.<ref name=":2" />&nbsp;Most species within this genus have polyps which are dimorphic:<ref>{{Cite book |last1=DeVictor |first1=Susan T. |title=Guide to the Shallow-Water (0-200m) Octocorals of the South Atlantic Bight |last2=Morton |first2=Steve L. |publisher=Magnolia Press |year=2010 |isbn=978-1-86977-584-1 |location=Auckland, NZ |chapter=Octocoral Morphology |chapter-url=https://www.dnr.sc.gov/marine/sertc/octocoral%20guide/octomorph.htm}}</ref> axial polyps grow rapidly and have lighter coloration, while radial polyps are small and are darker in coloration.<ref name=":2" /><ref>{{Cite book |last=Gilbert |first=Scott F |title=Developmental Biology |publisher=Sinauer Associates |year=2000 |isbn=0-87893-243-7 |edition=6th |location=Sunderland, MA |chapter=Embryonic Development |chapter-url=https://www.ncbi.nlm.nih.gov/books/NBK10120}}</ref> In the ''Acropora'' genus, [[Gamete|gamete synthesis]] and [[photosynthesis]] occur at the basal<ref>{{Cite journal |last1=Eric M |first1=Engstrom |last2=Izhaki |first2=Anat |last3=Bowman |first3=John L |date=July 2004 |title=Promoter Bashing, microRNAs, and Knox Genes. New Insights, Regulators, and Targets-of-Regulation in the Establishment of Lateral Organ Polarity in Arabidopsis |url=https://www.researchgate.net/figure/Four-axes-of-development-in-seed-plants-The-apical-basal-axis-1-of-the-plant_fig1_8500553 |journal=[[Plant Physiology (journal)|Plant Physiology]] |volume=135 |issue=2 |pages=685–694 |doi=10.1104/pp.104.040394 |pmid=15208415 |pmc=514105 |via=ResearchGate}}</ref> polyps, growth occurs mainly at the radial polyps. Growth at the site of the radial polyps encompasses two processes: [[asexual reproduction]] via [https://www.ncbi.nlm.nih.gov/books/NBK12640/ mitotic cell proliferation],<ref name=":2" /> and skeleton deposition of the calcium carbonate via [[Extracellular matrix|extra cellular matrix]] (EMC) proteins acting as [https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2354-4 differentially expressed (DE) signaling genes]<ref name=":2" /> between both branch tips and bases.&nbsp;These processes lead to [https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/cellular-differentiation colony differentiation], which is the most accurate distinguisher between coral species.<ref name=":1" /> In the Acropora genus, colony differentiation through [[Downregulation and upregulation|up-regulation and down-regulation]] of DEs.<ref name=":2" />

Systematic studies of soft coral species have faced challenges due to a lack of [[Taxonomy|taxonomic]] knowledge.<ref name=":1" />&nbsp;Researchers have not found enough variability within the genus to confidently delineate similar species, due to a low rate in mutation of [[mitochondrial DNA]].<ref>{{Cite journal |last1=Stemmer |first1=Kristina |last2=Burghardt |first2=Ingo |last3=Mayer |first3=Christoph |last4=Reinicke |first4=Götz B. |last5=Wägele |first5=Heike |last6=Tollrian |first6=Ralph |last7=Leese |first7=Florian |date=June 2013 |title=Morphological and genetic analyses of xeniid soft coral diversity (Octocorallia; Alcyonacea) |url=http://link.springer.com/10.1007/s13127-012-0119-x |journal=Organisms Diversity & Evolution |language=en |volume=13 |issue=2 |pages=135–150 |doi=10.1007/s13127-012-0119-x |bibcode=2013ODivE..13..135S |s2cid=17511020 |issn=1439-6092}}</ref>

Environmental factors, such as the rise of temperatures and acid levels in our oceans account for some [[speciation]] of corals in the form of [[Species loss|species lost]].<ref name=":2" />&nbsp;Various coral species have [[heat shock protein]]s (HSP) that are also in the category of DE across species.<ref name=":2" />&nbsp;These HSPs help corals combat the increased temperatures they are facing which lead to protein denaturing, growth loss, and eventually coral death.<ref name=":2" />&nbsp;Approximately 33% of coral species are on the International Union for Conservation of Nature's endangered species list and at risk of species loss.<ref>{{Cite web |title=Coral Reefs |url=https://www.iucn.org/theme/marine-and-polar/get-involved/coral-reefs |access-date=2022-04-27 |website=IUCN |language=en |url-status=dead |archive-url=https://web.archive.org/web/20220427041939/https://www.iucn.org/theme/marine-and-polar/get-involved/coral-reefs |archive-date=2022-04-27 }}</ref>&nbsp;[[Ocean acidification]] (falling pH levels in the oceans) is threatening the continued species growth and differentiation of corals.<ref name=":2" />&nbsp;Mutation rates of ''[[Vibrio]] shilonii'', the reef [[pathogen]] responsible for [[coral bleaching]], heavily outweigh the&nbsp;typical reproduction rates of coral colonies when pH levels fall.<ref name=":6">{{Cite journal |last1=Strauss |first1=Chloe |last2=Long |first2=Hongan |last3=Patterson |first3=Caitlyn E. |last4=Te |first4=Ronald |last5=Lynch |first5=Michael |date=2017-09-06 |editor-last=Moran |editor-first=Nancy A. |title=Genome-Wide Mutation Rate Response to pH Change in the Coral Reef Pathogen ''Vibrio shilonii'' AK1 |journal=mBio |language=en |volume=8 |issue=4 |pages=e01021–17 |doi=10.1128/mBio.01021-17 |doi-access=free |issn=2161-2129 |pmc=5565966 |pmid=28830944}}</ref> Thus, corals are unable to mutate their HSPs and other climate change preventative genes to combat the increase in temperature and decrease in pH at a competitive rate to these pathogens responsible for coral bleaching,<ref name=":6" /> resulting in species loss.