Mesophotic Coral Ecosystems (MCEs) are the continuation of the shallow water coral reefs into the twilight zone, at depth between 30 and 150m. These ecosystems are supporting a rich biodiversity into which light-dependent corals (Scleractinia Bourne, 1900) are among the dominant ecosystem engineers. Recent investigations on these ecosystems have shown that they support an exceptional biodiversity and often have high levels of endemism with numerous new species adapted to the low light environment. As MCEs are often located relatively farther away from the coastlines and deep below the sea surface, it has been suggested that they could face lower intensity and frequency of disturbances, providing temporary refuge for reefal organisms. MCEs could as well act as a source of propagules for shallow water communities, replenishing their populations following disturbances and thus facilitating the overall resilience of the ecosystem. In any case, the role that MCEs could play for future coral reefs is still debatable given the current extent of our knowledge about these ecosystems. In Taiwan for instance, there is very little information about the diversity in scleractinian corals below 30m in depth. Therefore, level of similarity between shallow and mesophotic biodiversity in scleractinian corals as well as the degree of genetic specialization with depth for these species are unknown. Lastly, the ability for mesophotic populations to serve as source of propagules has never been assessed, obscuring the role that MCEs could play for future Taiwanese coral reefs. The aim of this PhD project was to fill the gaps of knowledge about MCEs from Taiwan using Ludao (also called Green Island) as a reference. Investigation of the MCEs from Ludao, at depths between 38 and 60m, allowed the examination of low-gradient slopes associated with extended covers of sand and rubbles, which are known to limit the development of the MCEs. However, the presence of numerous small to large patches of hard substrates allows the development of a diverse scleractinian fauna. A minimum of 103 scleractinian species (plus two other reef-builders) were collected at mesophotic depths, including at least 12 new records for Taiwan. One scleractinian coral with large bathymetric distribution around the island (Pocillopora verrucosa Elis & Solander, 1786) was used as a model to investigate possible genetic specialization and population differentiation with depth, and to estimate levels of migration between shallow and deep zones. First, the use of molecular taxonomic markers on P. verrucosa collected from three locations at depth ranging from 7 to 45m excluded the presence of any genetic specialization related to depth. Then, the use of microsatellites markers to analyze the same specimens show little to no differentiation with depth, but rather a unique population pool with recent vertical (among depth) and horizontal (between sites) migration signals. These results suggest that P. verrucosa from Ludao is a panmictic population. Despite the relatively limitated MCEs development around Taiwan, these ecosystems around Ludao support a rich diversity in scleractinian corals species, and among all P. verrucosa harbors high levels of genetic diversity along its bathymetric distribution with vertical and horizontal migration. MCEs from Ludao could potentially act as a refuge and contribute to the replenishment of the shallow water populations following major disturbances, thus benefiting the ecosystem resilience. However, the role of potential refuge is demonstrated here for only one species and, despite potentially concerning species with similar life history traits at the same location, this role should now be investigated for other scleractinian species and other taxa in order to evaluate if future coral reefs of Taiwan could be functionally similar to their contemporary reefs. In conclusion, this study illustrates how the integration of molecular tools is of great importance to evaluate MCEs’ role for future coral reefs and further suggests MCEs around Taiwan should receive more attention and protection, especially in the context of rapid decline of the shallow water coral reefs.

Abdelkarim J, Robertson BC, Stanton JAL, Gemmell NJ (2009) Fast, cost-effective development of species-specific microsatellites markers by genome sequencing. Biotechniques 46(3): 185-192
Appeldoorn R, Ballantine D, Bejarano I Carlo M, Nemeth M, Otero E, Pagán F, Ruiz H, Schizas N, Sherman C, Weil E (2016) Mesophotic coral ecosystems under anthropogenic stress: a case study at Ponce, Puerto Rico. Coral Reefs 35(1): 63-75
Armstrong RA, Pizarro O, Roman C (2019) Underwater robotic technology for imaging mesophotic coral ecosystems. In: Loya Y, Puglise KA, Bridge T, eds. Mesophotic coral ecosystems of the world. Springer, Cham. pp 973-988
Baird AH, Madin JS, Álvarez-Noriega M, Fontoura L, Kerry JT, Kuo CY, Precoda K, Torres-Pulliza D, Woods RM, Zawada KJA, Hughes TP (2018) A decline in bleaching suggests that depth can provide a refuge from global warming in most coral taxa. Marine Ecology Progress Series 603: 257-264
Bak RPM, Nieuwland G, Meesters EH (2005) Coral reef crisis in deep and shallow reefs: 30 years of constancy and change in reefs of Curacao and Bonaire. Coral Reefs 24(3): 475-479
Baker EK, Puglise KA, Harris PT (2016) Mesophotic Coral Ecosystems – A lifeboat for coral reefs? The United Nations Environment Programme and GRID-Arendal, Nairobi and Arendal. 98 p
Bandelt HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16(1): 37-48
Barbará T, Palmas-Silva C, Paggi GM, Bered F, Fay MF, Lexer C (2007) Cross-species transfer of nuclear microsatellites markers: potential and limitations. Molecular Ecology 16: 3759-3767
Baums IB, Miller MW, Hellberg ME (2006) Geographic variation in clonal structure in a reef-building Caribbean coral, Acropora palmata. Ecological Monographs 76(4): 503-519
Bejarano L, Appeldoorn RS, Nemeth M (2014) Fishes associated with mesophotic coral ecosystems in La Parguera, Puerto Rico. Coral Reefs 33(2): 313-328
Bellwood DR, Hughes TP (2001) Regional-scale assembly rules and biodiversity of coral reefs. Science 292(5521): 1532-1535
Bellwood DR, Hughes TP, Folke C, Nyström N (2004) Confronting the coral crisis. Nature 429(6994): 827-833
Benzoni F, Stefani F, Pichon M, Galli P (2010) The name game: morpho-molecular species boundaries in the genus Psammocora (Cnidaria, Scleractinia). Zoological Journal of the Linnean Society 160(3): 421-456
Bongaerts P, Carmichael M, Hay KB, Tonk L, Frade PR, Hoegh-Guldberg O (2015) Prevalent endosymbiont zonation shapes the depth distributions of scleractinian coral species. Royal Society Open Science 2(2): 140297
Bongaerts P, Frade PR, Ogier JJ, Hay KB, van Bleijswijk J, Englebert N, Vermeij MJA, Bak RPM, Visser PM, Hoegh-Guldberg O (2013) Sharing the slope: depth partitioning of agariciid corals and associated Symbiodinium across shallow and mesophotic habitats (2–60 m) on a Caribbean reef. BMC Evolutionary Biology 13: 205
Bongaerts P, Ridgway T, Sampayo EM, Hoegh-Guldberg O (2010) Assessing the ‘deep reef refugia’ hypothesis: focus on Caribbean reefs. Coral Reefs 29: 309-327
Bongaerts P, Riginos C, Brunner R, Englebert N, Smith SR, Hoegh-Guldberg O (2017) Deep reefs are not universal refuges: Reseeding potential varies among coral species. Science Advances 3(2): e1602373
Bongaerts P, Riginos C, Hay KB, van Oppen MJ, Hoegh-Guldberg O, Dove S (2011) Adaptive divergence in a scleractinian coral: physiological adaptation of Seriaopora hystrix to shallow and deep reef habitats. BMC Evolutionary Biology 11: 303
Bongaerts P, Smith TB (2019) Beyond the “Deep Reef Refuge” hypothesis: a conceptual framework to characterize persistence at depth. In: Loya Y, Puglise KA, Bridge TCL (eds) Mesophotic Coral Ecosystems, Springer, Cham. pp881-896
Boogert NJ, Paterson DM, Laland KN (2006) The implications of niche construction and ecosystem engineering for conservation biology. BioScience 56: 570-578
Bouchon C (1981) Quantitative study of the scleractinian coral communities of a fringing reef of Reunion Island (Indian Ocean). Marine Ecology Progress Series 4: 273-288
Brazeau DA, Lesser MP, Slattery M (2013) Genetic structure in the coral, Montastraea cavernosa: assessing genetic differentiation among and within mesophotic reefs. PLoS ONE 8: e65845
Bridge T, Guinotte J (2012) Mesophotic coral reef ecosystems in the Great Barrier Reef World Heritage area: their potential distribution and possible role as refugia from disturbance. Great Barrier Reef Marine Park Authority, Townsville. 51p
Bridge T, Hoey A, Campbell S, Muttaqin E, Rudi E, Fadli N, Baird A (2014) Depth-dependent mortality of reef corals following a severe bleaching event: implications for thermal refuges and population recovery. F1000 Research 2: 187
Bridge TCL, Done TJ, Beaman RJ, Friedman A, Williams SB, Pizarro O, Webster JM (2011a) Topography, substratum and benthic macrofaunal relationships on a tropical mesophotic shelf margin, central Great Barrier Reef, Australia. Coral Reefs 30(1): 143-153
Bridge TCL, Done TJ, Friedman A, Beaman RJ, Williams SB, Pizarro O, Webster JM (2011b) Variability in mesophotic coral reef communities along the Great Barrier, Australia. Marine Ecology Progress Series 428: 63-75
Bridge TCL, Fabricius KE, Bongaerts, Wallace CC, Muir PR, Done TJ, Webster JM (2012) Diversity of Scleractinia and Octocorallia in mesophotic zone of the Great Barrier Reef, Australia. Coral Reefs 31(1): 179-189
Bridge TCL, Hughes TP, Guinotte JM, Bongaerts P (2013) Call to protect all coral reefs. Nature Climate Change 3(6): 528-530
Bruno JF, Côté IM, Toth LT (2019) Climate change, coral loss, and the curious case the parrotfish paradigm: why don’t marine protected areas improve reef resilience? Annual review of Marine Science 11: 307-334
Budd AF, Romano SL, Smith ND, Barbeitos MS (2010) Rethinking the phylogeny of scleractinian corals: a review of morphological and molecular data. Integrative and Comparative Biology 50: 411-427
Burke L, Reytar K, Spalding M, Perry A (2011) Reefs at risk revisited. Washington DC: World Resources Institute. 114p
Cacciapagla C, van Woesik R (2015) Reef-coral refugia in a rapidly changing ocean. Global Change Biology 21: 2272-2282
Cesar H, Burke L, Pet-Soede L (2003) The economics of worldwide coral reef degradation. Cesar Environmental Economics Consulting and WWF-Netherlands, Arnhem and Zeist, the Netherlands. 23p
Chapuis MP, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Molecular Biology and Evolution 24(3): 621-631
Chen C, Dai CF, Plathong S, Chiou CY, Chen CA (2008) The complete mitochondrial genomes of needle corals, Seriatopora spp. (Scleractinia: Pocilloporidae): an idiosyncratic atp8, duplicated trnW gene, and hypervariable regions used to determine species phylogenies and recently diverged populations. Molecular Phylogenetics and Evolution 46: 19-33
Chen CA, Shashank K (2009) Taiwan as a connective stepping-stone in the Kuroshio Traiangle and the conservation of coral ecosystems under the impacts of climate change. Kuroshio Science 3(1): 15-22
Chiazzari B, Magalon H, Gélin P, Macdonald A (2019) Living on the edge: Assessing the diversity of South African Pocillopora on the margins of the Southwestern Indian Ocean. PLoS ONE 14(8): e0220477
Chollet I, Mumby PJ (2013) Reefs of last resort: Locating and assessing thermal refugia in the wider Caribbean. Biological Conservation 167: 179-186
Colin PL (2016) Spotlight on the Palau Island group. In: Baker EK, Puglise KA, Harris PT (eds) Mesophotic coral ecosystems – a lifeboat for coral reefs? The United Nations Environment Programme and GRID-Arendal, Nairobi. pp 31-36
Colin PL, Devaney DM, Hillis-Colinvaux L, Suchanek TH, Harrison JT (1986) Geology and biological zonation of the reef slope, 50-360 m depth at Enewatak Atoll, Marshall Islands. Bulletin of Marine Science 38: 111-128
Cooper TF, Ulstrup KE, Dandan SS, Heyward AJ, Kuhl M, Muirhead A, O’Leary RA, Ziersen BE, van Oppen MJH (2011) Niche specialization of reef-building corals in the mesophotic zone: metabolic trade-offs between divergent Symbiodinium types. Proceeding of the Royal Society B: Biological Sciences 278: 1840-1850
Cowen RK, Sponaugle S (2009) Larval disprsal and marine population connectivity. Annual Review in Marine Science 1: 443-466
Crooks L, Carlborg Ö, Marklund S, Johansson AM (2013) Identification of null alleles and deletions from SNP genotypes for an intercross between domestic and wild chicken. G3: Gene, Genome, Genetics 3(8): 1253-1260
Dai CF (2006) Distribution and species diversity of reef corals in Taiwan (II) Eastern Taiwan. Fisheries Agent, Council of Agriculture, Taipei. (In Chinese)
Dai CF (2007) Distribution and species diversity of reef corals in Taiwan (III) Southern Taiwan including Xiaoliuchiu. Fisheries Agent, Council of Agriculture, Taipei. (In Chinese)
Dai CF, Horng S (2009a) Scleractinia fauna of Taiwan I. The complex group. Taipei: National Taiwan University. 172p
Dai CF, Horng S (2009b) Scleractinia fauna of Taiwan II. The robust group. Taipei: National Taiwan University.
Dai CF, Soong K, Jeng MS, Chen CA, Fan TY (2004) Status of coral reefs of Taiwan. Fisheries Agent, Council of Agriculture, Taipei. (In Chinese)
Dai CF, Stewart LL, Cooper RA, Sprunk HJ (1992) Distribution of substrates and macrobenthos at depth between 35 and 120 m in southern Taiwan. Acta Oceanographica Taiwan 28: 1-18
Dakin EE, Avise JC (2004) Microsatellite null alleles in parentage analysis. Heredity 92: 504-509
Davis J, Pavlova A, Thompson RM, Sunnucks P (2013) Evolutionary refugia and ecological refuges: key concepts for conserving Australian arid zone freshwater biodiversity under climate change. Global Change Biology 19(7): 1970-1984
De Palmas S, Soto D, Denis V, Ho MJ, Chen CA (2018) Molecular assessment of Pocillopora verrucosa (Scleractinia; Pocilloporidae) distribution along a depth gradient in Ludao, Taiwan. PeerJ 6(1): e5797
De’ath G, Fabricius KE, Sweatman H, Puotinen M (2012) The 27-year decline of coral cover in the Great Barrier Reef and its causes. Proceedings of the National Academy of Sciences of the United States of America 109(44): 17995-17999
Denis V, De Palmas S, Benzoni F, Chen CA (2015) Extension of the known distribution and depth range of the scleractinian coral Psammocora stellata: first record from a Taiwanese mesophotic reef. Marine Biodiversity 45(4): 619-620
Denis V, Soto D, De Palmas S, Lin YTV, Benayahu Y, Huang YM, Liu SL, Chen JW, Chen Q, Sturaro N, Ho MJ, Su Y, Dai CF, Chen CA (2019) Taiwan. In: Loya Y, Puglise KA, Bridge TCL (eds) Mesophotic coral ecosystems of the world. Springer, Cham. pp 249-264
Dobrowski SZ (2011) A climatic basis for microrefugia: the influence of terrain on climate. Global Change Biology 17: 1022-1035
Done TJ (2011) Corals: environmental controls on growth. In: Hopley D (ed) Encyclopedia of modern coral reefs. Springer, Dordrecht, Netherlands. pp 281-293
Dumalagan Jr EE, Cabaitan PC, Bridge TCL, Go KT, Quimpo TJR, Olavides RDD, Munar JC, Villanoy CL, Siringan FP (2019) Spatial variability in benthic assemblage composition in shallow and upper mesophotic coral ecosystems in the Philippines. Marine Environmental Research 150: 104772
Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4(2): 359-361
Eckert RJ, Studivan MS, Voss JD (2019) Populations of the coral species Montastraea cavernosa on the Belize Barrier Reef lack vertical connectivity. Scientific Reports 9: 7200
Edmunds PJ, Adjeroud M, Basket ML, Baums IB, Budd AF, Carpenter RC, Fabina NS, Fan TY, Franklin EC, Gross K, Han X, Jacobson L, Klaus JS, McClanahan TR, O’Leary JK, van Oppen MJH, Pochon Z, Putnam HM, Smith TB, Stat M, Sweatman H, van Woesik R, Gates RD (2014) Persistence and change in community composition of reef corals through present, past, and future climates. PLoS ONE 9(10): e107525
Einbinder S, Mass T, Brokovitch E, Dubinsky Z, Erez J, Tchernov D (2009) Changes in morphology and diet of the coral Stylophora pistillata along a depth gradient. Marine Ecology Progress Series 381: 167-174
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611-2620
Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10: 564-567
Eyal G, Wiedenmann J, Grinblat M, D’Angelo C, Kramarsky-Winter E, Treibitz T, Ben-Zvi O, Shaked Y, Smith TB, Harii S, Denis V, Noyes T, Tamir R, Loya Y (2015) Spectral diversity and regulation of coral fluorescence in a mesophotic reef habitat in the Red Sea. PLoS ONE 10: e0128697
Eytan RI, Hayes M, Arbour-Reily P, Miller M, Hellberg ME (2009) Nuclear sequences reveal mid-range isolation of an imperiled deep-water coral population. Molecular Ecology 18: 2375-2389
Falkowski PG, Dubinsky Z (1981) Light-shade adaptation of Stylophora pistillata, a hermatypic coral from the Gulf of Eilat. Nature 289: 172-174
Fine M, Gildor H, Genin A (2013) A coral reef refuge in the Red Sea. Global Change Biology 19(12): 3640-3647
Flot JF, Magalon H, Cruaud C, Couloux A, Tillier (2008) Patterns of genetic structure among Hawaiian corals of the genus Pocillopora yield clusters of individuals that are compatible with morphology. Comptes Rendus Biologies 331: 239-247
Forsman ZH, Barshis DJ, Hunter CL, Toonen RJ (2009) Shape-shifting corals: molecular markers show morphology is evolutionarily plastic in Porites. BMC Evolutionary Biology 9: 45
Frade PR, Bongaerts P, Englebert N, Rogers A, Gonzalez-Rivero M, Hoegh-Guldberg O (2018) Deep reefs of the Great Barrier Reef offer limited thermal refuge during mass coral bleaching. Nature Communications 9: 3447
Friecke HW, Meishner D (1985) Depth limits of Bermudan scleractinian corals: a submersible survey. Marine Biology 88: 175-187
Friecke HW, Vareshi E, Schlichter D (1987) Photoecology of the coral Leptoseris fragilis in the Red Sea twilight zone (an experimental study by submersible). Oecologia 73: 371-381
Frieler K, Meinshausen M, Golly A, Mengel M, Lebek K, Donner SD, Hoegh-Guldberg (2013) Limiting global warming to 2 °C is unlikely to save most coral reefs. Nature Climate Change 3: 165-170
Gélin P, Fauvelot C, Bigot L, Baly J, Magalon H (2017a) From population connectivity to the art of striping Russian dolls: the lessons from Pocillopora corals. Ecology and Evolution 8(2): 1411-1426
Gélin P, Postaire B, Fauvelot C, Magalon H (2017b) Reevaluating species number, distribution and endemism of the coral genus Pocillopora Lamarck, 1816 using species delimitation methods and microsatellites. Molecular Phylogenetics and Evolution 109: 430-446
Gilmore RG Jr (2016) You can’t catch a fish with a robot. Gulf and Caribbean Research 27(1): ii-xiv
Glynn P (1974) Rolling stones among the scleractinia: Mobile coralliths in the Gulf of Panama. Proceedings of the second International Coral Reef Symposium 2: 183-198
Glynn PW (1996) Coral reef bleaching: facts, hypotheses and implications. Global Change Biology 2: 495-509
Goetze JS, Langlois TJ, Egli DP, Harvey ES (2011) Evidence of artisanal fishing impacts and depth refuge in assembles of Fijian reef fish. Coral Reefs 30(2): 507-517
Goreau TF, Goreau NI (1959) The physiology of skeleton formation in corals. I. A method for measuring the rate of calcium deposition by corals under different conditions. Biological Bulletin 116: 59-75
Goreau TF, Land LS (1974) Fore-reef morphology and depositional processes, North Jamaica. In: Laporte LF (ed) Reefs in time and space, volume 18. Special Publication of the Society of Economic Paleontologists and Mineralogists, Tusla, 77-89
Gorospe KD, Karl SA (2015) Depth as an organizing force in Pocillopora damicornis: Intra-reef genetic architecture. PLoS ONE 10(3): e0122127
Goodbody-Gringley G, Noyes T, Smith SR (2019) Bermuda. In: Loya Y, Puglise KA, Bridge TCL (eds) Mesophotic coral ecosystems of the world. Springer, Cham. pp 31-45
Graham NAJ, Chong-Seng KM, Huchery C, Januchowski-Hartley FA, Nash KL (2014) Coral reef community composition in the context of disturbances history on the Great Barrier Reef, Australia. PLoS ONE 9(7): e101204
Gress E, Arroyo-Gerez M, Wright G, Andradi-Brown DA (2016) Mesophotic Coral Ecosystems (MCEs) act as Deep Reef Refuges for fish populations in Cozumel, Mexico. Proceedings of the 69th Gulf and Caribbean Fisheries Institute: 85-86
Guest JR, Edmunds PJ, Gates RD, Kuffner IB, Andersson AJ, Barnes BB, Chollett I, Courtney TA, Elhi R, Gross K, Lenz EA, Mitarai S, Mumby PJ, Nelson HR, Parker BA, Putnam HM, Rogers CS, Toth LT (2018) A framework for identifying and characterizing coral reef “oases” against a backdrop of degradation
Guichoux E, Lagache L, Wagner S, Chaumeil P, Léger P, Lepais O, Lepoittevin C, Malausa T, Revardel E, Salin F, Petit RJ (2011) Current trends in microsatellite genotyping. Molecular Ecology Resources 11(4): 591-611
Guinote JM, Fabry VJ (2008) Ocean acidification and its potential effects on marine ecosystems. Annals of the New York Academy of Sciences 1134: 320-342
Hammerman NM, Rivera-Vicens RE, Galaska MP, Weil E, Appledoorn RS, Alfaro M, Schizas NV (2018) Population connectivity of the plating coral Agaricia lamarcki from southwest Puerto Rico. Coral Reefs 37:183-191
Hanski I (1999) Metapopulation ecology. Oxford University Press. 319p
Harborne AR, Rogers A, Bozec YM, Mumby PJ (2017) Multiple stressors and the functioning of coral reefs. Annual Review of Marine Science 9: 445-468
Harris PT, Bridge TCL, Beaman RJ, Webster JM, Nichol SL, Brooke BP (2013) Submerged banks in the Great Barrier Reef, Australia, greatly increase available coral reef habitat. ICES Journal of Marine Science, 70(2): 284-293
Hennige SJ, Burdett HL, Perna G, Tudhope AW, Kamenos NA (2017) The potential for coral reef establishment through free-living stabilization. Scientific Reports 7: 13322
Hinderstein L, Marr JCA, Martinez FA, Dowgiallo MJ, Puglise KA, Pyle RL, Zawada DG, Appeldoorn R (2010) Theme section on “Mesophotic coral ecosystems: characterization, ecology, and management.” Coral Reefs 29(2): 247-251
Hoegh-Guldberg O (2004) Coral reefs and projections of future change. In: Rosenberg E & Loya Y (Eds) Coral Health and Disease. Springer, Berlin, Heidelberg. pp 463-484
Hoegh-Guldberg O, Mumby PJ, Hooten AJ, Steneck RS, Greenfield P, Gomez E, Harvell CD, Sale PF, Edwards AJ, Caldeira K, Knowlton N, Eakin CM, Iglesias-Prieto R, Muthiga N, Bradhury RH, Dubi A, Hatziolos ME (2007) Coral reefs under rapid climate change and ocean acidification. Science 318(5857): 1732-1742
Hoeksema BW (1989) Taxonomy, phylogeny and biogeography of mushroom corals (Scleractinia: Fungiidae). Zoologische Verhandelingen 254: 1-295
Hoeksema BW (2014) The “Fungia patella group” (Scleractinia: Fungiidae) revisited with a description of the mini mushroom coral Cycloseris boschmai sp. n. Zookeys 371: 57-84
Holstein DM, Paris CB, Vaz AC, Smih TB (2016) Modeling vertical coral connectivity and mesophotic refugia. Coral Reefs 35(1): 23-37
Holstein DM, Smith TB, Gyory J, Paris CB (2015) Fertile fathoms: Deep reproductive refugia for threatened shallow corals. Scientific Reports 5: 12407
Holstein DM, Smith TB, Paris CB (2016) Depth-independent reproduction in the reef coral Porites astreoides from shallow to mesophotic zones. PLoS ONE 11(1): e0146068
Hoogenboom MO, Connolly SR, Anthony KRN (2008) Interactions between morphological and physiological plasticity optimize energy acquisition in corals. Ecology 89: 1144-1154
Hoskin CM, Reed JK, Mook DH (1986) Production and off-bank transport of carbonate sediment, Black Rock, southwest Little Bahama Bank. Marine Geology 73(1-2): 125-144
Hsu CM, de Palmas S, Kuo CY, Denis V, Chen CA (2014) Identification of scleractinian coral recruits using fluorescent censusing and DNA barcoding techniques. PLoS ONE 9(9): e107366
Huang DW, Licuanan WY, Hoeksema BW, Chen CA, Ang PO, Huang Hui, Lane DJW, Vo ST, Waheed Z, Affendi YA, Yeemin T, Chou LM (2014) Extraordinary diversity of reef corals in the South China Sea. Marine Biodiversity 45(2): 157-168
Hughes TP, Anderson KD, Conolly SR, Heron SF, Kerry JT, Lough JM, Baird AH, Baum JK, Berumen ML, Bridge TC, Claar DC, Eakin CM, Gilmour JP, Graham NAJ, Harrison H, Hobbs JPA, Hoey AS, Hoogenboom M, Lowe RJ, McCulloch MT, Pandolfi JM, Pratchett M, Schoepf V, Torda G, Wilson SK (2018) Spatial and temporal patterns of mass bleaching of corals in the Anthropocene. Science 359(6371): 80-83
Hughes TP, Baird AH, Bellwood DR, Card M, Connolly SR, Folke C, Grosberg R, Hoegh-Guldberg O, Jackson JB, Kleypas J, Lough JM, Marshall P, Nyström M, Palumbi SR, Pandolfi JM, Rosen B, Roughgarden J (2003) Climate change, human impacts, and the resilience of coral reefs. Science 301(5635): 929-933
Hughes TP, Barnes ML, Bellwood DR, Cinner JE, Cumming GS, Jackson JB, Kleypas J, van de Leemput IA, Lough JM, Morrison TH, Palumbi SR, van Nes EH, Scheffer M (2017a) Coral reefs in the Anthropocene. Nature 546: 82-90
Hughes TP, Kerry JT, Álvarez‐Noriega M, Álvarez‐Romero JG, Anderson KD, Baird AH, Babcock RC, Beger M, Bellwood DR, Berkelmans R, Bridge TC, Butler IR, Byrne M, Cantin NE, Comeau S, Conolly SR, Cumming GS, Dalton SJ, Diaz-Pulido G, Eakin CM, Figueira WF, Gilmour JP, Harrison HB, Heron SF, Hoey A, Hobbs JPA, Hoogenboom MO, Kennedy EV, Huo CY, Lough JM, Lowe RJ, Liu G, McCulloch MT, Malcolm HA, McWilliam MJ, Pandolfi JM, Pears RJ, Pratchett MS, Schoepf V, Simpson T, Skirving WJ, Sommer B, Torda G, Wachenfeld DR, Willis BL, Wilson SK (2017b). Global warming and recurrent mass bleaching of corals. Nature 543: 373-377
Hughes TP, Tanner JE (2000) Recruitment failure, life histories, and long-term decline of Caribbean corals. Ecology 81: 2250-2263
Johnston EC, Forsman ZH, Flot JF, Schmidt-Roach S, Pinzón H, Knapp ISS, Toonen RJ (2017) A genomic glance through the fog of plasticity and diversification in Pocillopora. Scientific Reports 7(1): 5991
Johnston EC, Forsman ZH, Toonen RJ (2018) A simple molecular technique for distinguishing species reveals frequent misidentification of Hawaiian corals in the genus Pocillopora. PeerJ 6: e4355
Jones CG, Lawton JH, Shachak M (1997) Positive and negative effects of organisms as physical ecosystem engineers. Ecology 78: 1946-1957
Kahng SE, Akkaynak D, Shlesinger T, Hochberg EJ, Wiedenmann J,
Tamir R, Tchernov D (2019) Light, temperature, photosynthesis,
heterotrophy, and the lower depth limits of mesophotic coral ecosystems. In: Loya Y, Puglise KA, Bridge TCL (eds) Mesophotic
coral ecosystems. Springer, Cham. pp 801-828
Kahng SE, Copus JM, Wagner D (2014) Recent advances in the ecology of mesophotic coral ecosystems. Current Opinion in Environmental Sustainability 7: 72-81
Kahng SE, Garcia-Sais JR, Spalding HL, Brokovitch E, Wagner D, Weil E, Hinderstein L, Toonen RJ (2010) Community ecology of mesophotic coral ecosystems. Coral Reefs 29(2): 255-275
Karnauskas KB, Cohen AL (2012) Equatorial refuge amid tropical warming. Nature Climate Change 2: 530-534
Kavousi J, Keppel G (2017) Clarifying the concept of climate change refugia for coral reefs. ICES Journal of Marine Science 75(1): 43-49
Keppel G, Van Niel KP, Wardell‐Johnson GW, Yates CJ, Byrne M, Mucina L, Schut AGT, Hopper SD, Franklin SE (2012) Refugia: identifying and understanding safe havens for biodiversity under climate change. Global Ecology and Biogeography 21: 393-404
Keppel G, Wardell‐Johnson GW (2012) Refugia: keys to climate change management. Global Change Biology 18: 2389-2391
Keshavmurthy S, Yang SY, Alamaru A, Chuang YY, Pichon M, Obura DO, Fontana S, De Palmas S, Stefani F, Benzoni F, MacDonald A, Noreen AME, Chen C, Wallace CC, Moothein Pillay R, Denis V, Affendi YA, Reimer JD, Mezaki T, Sheppard CRC, Loya Y, Abelson A, Mohammed MA, Baker AC, Mostafavi PG, Suharsono BA, Chen CA (2013) DNA barcoding reveals the coral ‘laboratory-rat’, Stylophora pistillata encompasses multiple identities. Scientific Reports 3: 1520
Kirk JTO (1994) Light and photosynthesis in aquatic ecosystems. Cambridge University Press, New York. pp 509
Kopelman NM, Mayzel J, Jakobsson Mattias, Rosebberg N, Mayrose I (2015) CLUMPAK: a program for identifying clustering modes and mackaging population structure inferences across K. Molecular Ecology Resources 15(5): 1179-1191
Kramer N, Eyal G, Tamir R, Loya Y (2019) Upper mesophotic depths
in the coral reefs of Eilat, Red Sea, offer suitable refuge grounds for
coral settlement. Scientific Reports 9: 2663
Kritzer JP, Sale PF (2004) Metapopulation ecology in the sea: from Levin’s model to marine ecology and fisheries science. Fish and Fisheries 5(2): 131-140
Kubomura T, Yamashiro H, Reimer JD (2018) Appearance of an anomalous black band disease at upper mesophotic depths after coral bleaching. Diseases of aquatic organisms 131(3): 245-249
Kühlmann DHH (1983) Composition and ecology of deep-water coral associations. Helgoländer Meeresuntersuchungen 36: 183-204
Kumar S, Stecher G, Tamura K (2016) MEGA 7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33(7): 1870-1874
Lamb JB, Willis BL, Fiorenza EA, Couch CS, Howard R, Rader DN, True JD, Kelly LA, Ahmad A, Jompa J, Harvell D (2018) Plastic waste associated with dicease on coral reefs. Science 359(6374): 460-462
Laverick JH, Andradi-Brown DA, Exton DA, Bongaerts P, Bridge TCL, Lesser MP, Pyle RL, Slaterry M, Wagner D, Rogers AD (2016) To what extent do mesophotic coral ecosystems and shallow reefs share species of conservation interest? Environmental Evidence 5: 16
Laverick JH, Piango S, Andradi-Brown DA, Exton DA, Bongaerts P, Bridge TCL, Lesser MP, Pyle RL, Slaterry M, Wagner D, Rogers AD (2018) To what extent do mesophotic coral ecosystems and shallow reefs share species of conservation interest? A systematic review. Environmental Evidence 7: 15
Leigh JW, Bryant D (2015) POPART: full-feature software for haplotype network construction. Methods in Ecology and Evolution 6(9): 1110-1116
Lesser MP, Slattery M, Mobley CD (2009) Biodiversity and functional ecology of mesophotic coral reefs. Annual Review of Ecology, Evolution, and Systematics 49: 49-71
Lesser MP, Slattery M, Stat M, Ojimi M, Gates RD, Grottoli A (2010) Photoacclimatization by the coral Montastraea cavernosa in the mesophotic zone: light, food, and genetics. Ecology 91: 990-1003
Lesser MP, Weis VM, Patterson MR, Jokiel PL (1994) Effects of morphology and water motion on carbon delivery and productivity in the reef coral, Pocillopora damicornis (Linnaeus): diffusion barriers, inorganic carbon limitation, and biochemical plasticity. Journal of Experimental Marine Biology and Ecology 178(2): 153-79
Levitan DR, Fukami H, Jara J, Kline D, McGovern TM, McGhee KE, Swanson CA, Knowlton N (2004) Mechanisms of reproductive isolation among sympatric broadcast-spawning corals of the Montastraea annularis complex. Evolution 58(2): 308-323
Lewis JB (1988) Sperical growth in the Caribbean coral Siderastrea radians (Pallas) and its survival in disturbed habitats. Coral Reefs 7: 161-167
Liddell WD, Avery WE, Ohlhorst SL (1997) Patterns of benthic community structure, 10-250 m, the Bahamas. In: Lessios HA, Macintyre IG (eds) Proceedings of the 8th International Coral Reef Symposium. Smithsonian Tropical Research Institute, Panama. pp 437-442
Liddell WD, Ohlhorst SL (1988) Hard substrata community patterns, 1-120m, North Jamaica. Palaois 3(4): 413-423
Lin YV, Denis V (2019) Acknowledging differences: number, characteristics, and distribution of marine benthic communities along Taiwan coast. Ecosphere 10(7): e02803
Lindfield SJ, Harvey ES, Halford AR, McIlwain JL (2016) Mesophotic depths as refuge areas for fishery-targeted species on coral reefs. Coral Reefs 35: 125-137
Linfield SJ, McIlwain JL, Harvey ES (2014) Depth refuge and the impacts of SCUBA spearfishing on coral reef fishes. PLoS ONE 9(3): e92628
Locker S, Armstrong R, Battista T, Rooney J, Sherman C, Zawada D (2010) Geomorphology of mesophotic coral ecosystems: current perspectives on morphology, distribution, and mapping strategies. Coral Reefs 29: 329-345
Loreau M, Mouquet N (1999) Immigration and the maintenance of local species diversity. American Naturalist 154(4): 427-440
Loya Y, Eyal G, Treibitz T, Lesser MP, Appeldoorn R (2016) Theme section on mesophotic coral ecosystems: advances in knowledge and future perspectives. Coral Reefs 35(1): 1-9
MacDonald C, Bridge TCl, Jones GP (2016) Depth, bay position and habitat structure as determinants of coral reef fish distributions: are deep reefs a potential refuge? Marine Ecology Progress Series 561: 217-231
Madin JS, Anderson K, Andreason M, Bridge TCL, Cairns S, Connolly SR, Darling ES, Diaz M, Falster D, Franklin EC, Gates RD, Hoogenboom MO, Huang D, Keith SA, Kosnik M, Kuo C-Y, Lough JM, Lovelock CE, Luiz O, Martinelli J, Mizerek T, Pandolfi JM, Pochon X, Putnam HM, Pratchett MS, Roberts E, Stat M, Wallace CC, Widman E, Baird AH (2016) The Coral Trait Database, a curated database of trait information for coral species from the global oceans. Scientific Data 3: 160012
Magalon H, Samadi S, Richard M, Adjeroud M, Veuille M (2004) Development of coral and zooxanthella-specific microsatellites in three species of Pocillopora (Cnidaria, Scleractinia) from French Polynesia. Molecular Ecology Notes 4(2): 206-208
Magoulick DD, Kobza RM (2003) The role of refugia during drought: a review and synthesis. Freshwater Biology 48(7): 1186-1198
Mangubhai S, Souter P, Grahn M (2007) Phenotypic variation in the coral Platygyra daedalea in Kenya: morphometry and genetics. Marine Ecology Progress Series 345: 105-115
Maragos JE, Jokiel P (1986) Reef corals of Johnston Atoll: one of the world’s most isolated reefs. Coral Reefs 4: 141-150
Marcelino LA, Westneat MW, Stoyneva V, Henss J, Rogers JD, Radosevich A, Turzhitsky V, Siple M, Fang A, Swain TD, Fung J, Backman V (2013) Modulation of light-enhancement to symbiotic algae by light-scattering in corals and evolutionary trends in bleaching. PLoS ONE 8: e61492
Marti-Puig P, Forsman ZH, Haverkort-Yeh RD, Knapp IS, Maragos JE, Toonen RJ (2014) Extreme phenotypic polymorphism in the coral genus Pocillopora; micro-morphology corresponds to mitochondrial groups, while colony morphology does not. Bulletin of Marine Science 90(1): 211-31
Mayfield AB, Hsiao YY, Fan TY, Chen CS, Gates RD (2010) Evaluating the temporal stability of stress-activated protein kinase and cytoskeleton gene expression in the Pacific reef corals Pocillopora damicornis and Seriatopora hystrix. Journal of Experimental Biology and Ecology 395(1-2): 215-222
McCook LJ, Almany GR, Berumen ML, Day JC, Green AL, Jones GP, Leis JM, Planes S, Russ GR, Sale PF, Thorrold SR (2009) Management under uncertainty: guide-lines for incorporating connectivity into the protection of coral reefs. Coral Reefs 28: 353-366
Medina M, Weil E, Szmant AM (1999) Examination of the Montastraea annularis species complex (Cnidaria: Scleractinia) using ITS and COI sequences. Marine Biotechnology 1: 89-97
Morais J, Santos BA (2018) Limited potential of deep reefs to serve as refuges for tropical Southwestern Atlantic corals. Ecosphere 9(7): e02281
Muir PR, Pichon M (2019) Biodiversity of reef-building, scleractinian corals. In: Loya Y, Puglise KA, Bridge T, eds. Mesophotic coral ecosystems of the world. Springer, Cham. pp589-620
Muir PR, Wallace CC, Done T, Aguirre JD (2015) Limited scope for latitudinal extension of reef corals. Science 348: 1135-1138
Muscatine I, Goiran C, Land L, Jaubert J, Cuif JP, Allemand D (2005) Stable isotope (δ13C and δ15N) of organic matrix from coral skeleton. Proceedings of the National Academy of Sciences of the United States of America 102: 1525-1530
Nakajima Y, Wepfer PH, Suzuki S, Zayasu Y, Shinzato C, Satoh N, Mitarai S (2017) Microsatellite markers for multiple Pocillopora genetic lineages offer new insights about coral populations. Scientific Reports 7: 6729
Nir O, Gruber DF, Shemesh E, Glasser E, Tchernov D (2014) Seasonal mesophotic coral bleaching of Stylophora pistillata in the Northern Red Sea. PLoS ONE 9(1): e84968
Norström AV, NyströmM, Jouffray JB, Folke C, Graham NAJ, Moberg F, Olsson P, Williams GJ (2016) Guiding coral reef fuures in the Anthropocene. Frontiers in Ecology and the Environment 14(9): 490-498
Ohlhorst SL, Liddell WD (1988) The effect of substrata microtopography on reef community structure, 60–120 m. In: Choat JH, Barnes D, Borowitzka MA et al (eds) Proceedings of the Sixth International Coral Reef Symposium. Townsville, Australia. pp 355-360
Paetkau A, Slade R, Burden M, Estoup A (2004) Genetic Assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of occuracy and power. Molecular Ecology 13: 55-65
Paetkau D, Strobeck C (1995) The molecular basis and evolutionary history of a microsatellite null allele in bears. Molecular Ecology 4: 519-520
Paz-García DA, Hellberg ME, García-de-LeónFJ, Balart EF (2015) Switch between morphospecies of Pocillopora corals. The American Naturalist 186(3): 434-440
Peakall R, Smouse PE (2012) GenAIEx 6.5: genetic analysis in Excel. Populations genetic software for teaching and research–an update. Bioinformatics 28(19): 2537-2539
Perry CT, Alvarez-Filip L (2019) Changing geo-ecological functions of coral reefs in the Anthropocene. Functional Ecology 33(6): 976-988
Pinheiro HT, Goodbody-Gringley G, Jessup ME, Shepherd B, Chequer AD, Rocha LA (2016) Upper and lower mesophotic coral reef fish communities evaluated by underwater visual censuses in two Caribbean locations. Coral Reefs 35(1): 139-151
Pinzon JH, LaJeunesse TC (2011) Species delimitation of common reef corals in the genus Pocillopora using nucleotide sequence phylogenies, population genetics and symbiosis ecology. Molecular Ecology 20(2): 311-325
Pinzón JH, Sampayo E, Cox E, Chauka LJ, Chen CA, Voolstra CR, LaJeunesse TC (2013) Blind to morphology: genetics identifies several widespread ecologically common species and few endemics among Indo‐Pacific cauliflower corals (Pocillopora, Scleractinia). Journal of Biogeography 40: 1595-1608
Piry S, Alapetite A, Cornuet JM, Paetkau D, Baudouin L, Estoup A (2004) Geneclass 2: A Software for genetic assignment and first-generation migrant detection. Journal of Heredity 95: 536-539
Pochon X, Forsman ZH, Spalding HL, Padilla-Gamiño JL, Smith CM, Gates RD (2015) Depth specialization in mesophotic corals (Leptoseris spp.) and associated algal symbionts in Hawai’i. Royal Society Open Science 2(2): 140351
Poquita-Du RC, Ng CSL, Loo JB, Afiq-Rosli L, Tay YC, Todd PA, Chou LM, Huang D (2017) New evidence shows that Pocillopora ‘damicornis-like’ corals in Singapore are actually Pocillopora acuta (Scleractinia: Pocilloporidae). Biodiversity Data Journal 5: e11407
Prada C, Hellberg ME (2013) Long prereproductive selection and divergence by depth in a Caribbean candelabrum coral. Proceeding of Natural Academy of Sciences 110: 3961-3966
Prada C, Schizas NV, Yoshioka PM (2008) Phenotypic plasticity or speciation? A case from a clonal marine organism. BMC Evolutionary Biology 8: 47
Prasetia R, Sinniger F, Hashizume K, Harii S (2017) Reproductive biology of the deep brooding coral Seriatopora hystrix: implications for shallow reef recovery. PLoS ONE 12(5): e017034
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959
Puglise KA, Hinderstein LM, Marr JCA, Dowgiallo MJ, Martinez FA (2009) Mesophotic coral ecosystems research strategy: International workshop to prioritize research and management needs for mesophotic coral ecosystems, Jupiter, Florida, 12-15 July 2008. Silver Spring, MD: NOAA National Centers for Coastal Ocean Science, Center for Sponsored Coastal Ocean Research, and Office of Ocean Exploration and Research, NOAA Undersea Research Program. NOAA Technical Memorandum NOS NCCOS 98 and OAR OER 2. 24p
Putnam HM, Gates RD (2015) Preconditioning in the reef-building coral Pocillopora damicornis and the potential for trans-generational acclimatization in coral larvae under future climate change conditions. Journal of Experimental Biology 218(15): 2365-2372
Pyle RL (2019) Advanced technical diving. In: Loya Y, Puglise KA, Bridge T, eds. Mesophotic coral ecosystems of the world. Springer, Cham. pp 959-972
Pyle RL, Copus JM (2019) Mesophotic Coral Ecosystems: introduction and overview. In: Loya Y, Puglise KA, Bridge T, eds. Mesophotic coral ecosystems of the world. Springer, Cham. pp 3-27
Reed JK (1985) Deepest distribution of Atlantic hermatypic corals discovered in the Bahamas. Proceeding of the 5th International Coral Reef Symposium 6: 249-254
Reyes-Bonilla, H., J. T. Ketchum-Mejia, G. Cruz-Piñón y E. Barjau-González (2005) Catálogo de corales pétreos (Anthozoa: Scleractinia) depositados en el Museo de Historia Natural de la Universidad Autónoma de Baja California Sur. La Paz: Universidad Autónoma de Baja California Sur.
Ribas-Deulofeu L, Denis V, De Palmas S, Kuo CY, Hsieh HJ, Chen CA (2016) Structure of benthic communities along the Taiwan latitudinal gradient. PLoS ONE 11: e0160601
Richards ZT, Bryce M, Bryce C (2013) New records in atypical coral reef habitat in the Kimberley, Australia. Journal of Marine Biology 363894
Rico C, Rico I, Hewitt G (1996) 470 million years of conservation of microsatellite loci among fish species. Proceeding of the Royal Society B: Biological Sciences 263: 549-557
Ridgway T, Hoegh-Guldberg O (2002) Reef recovery in disturbed coral reef ecosystems. Proceedings of 9th International Coral Reef Symposium 2: 1117-1122
Ridgway T, Riginos C, Davis J, Hoegh-Guldberg O (2008) Genetic connectivity patterns of Pocillopora verrucosa in southern African Marine Protected areas. Marine Ecology Progress Series 354: 161-168
Riegl B, Bruckner A, Coles SL, Renaud P, Dodge RE (2009) Threats and conservation in an era of global change. Annals of the New York Academy of Sciences 1162: 136-186
Riegl B, Piller WE (2003) Possible refugia for reefs in times of environmental stress. International Journal of Earth Sciences 92: 520-531
Robitzch V, Banguera-Hinestroza EB, Sawall Y, Al-Sofyani A, Voolstra CR (2015) Absence of genetic differentiation in the coral Pocillopora verrucosa along environmental gradients of the Saudi Arabian Red Sea. Frontiers in Marine Sciences 2(5)
Rocha LA, Pinheiro HT, Shepherd B, Papastamatiou YP, Luiz OJ, Pyle RL, Bongaerts P (2018) Mesophotic coral ecosystems are threatened and ecologically distinct from shallow water reefs. Science 361(6399): 281-284
Rodriguez-Martinez RE, Jordan-Dahlgren E (1999) Epibiotic and free-living Porites astreoides. Coral Reefs 18: 159-161
Roff G (2008) Corals on the move: morphological and reproductive strategies of reef flat coralliths. Coral Reefs 27: 343-344
Rooney J, Donham E, Montgomery A, Spalding H, Parrish F, Boland R, Fenner D, Gove J, Vetter O (2010) Mesophotic coral ecosystems in the Hawaiian Archipelago. Coral Refs 29:361-367
Schmidt‐Roach S, Lundgren P, Miller K, Gerlach G, Noreen A, Andreakis N (2012) Assessing hidden species diversity in the coral Pocillopora damicornis from Eastern Australia. Coral Reefs 32: 1-12
Schmidt-Roach S, Miller KJ, Lundgren P, Andreakis N (2014) With eyes wide open: a revision of species within and closely related to the Pocillopora damicornis species complex (scleractinian; Pocilloporidae) using morphology and genetics. Zoological Journal of the Linnean Society 170 (1): 1-33
Semmler RF, Hoot WC, Reaka ML (2017) Are mesophotic coral ecosystems distinct communities and can they serve as refugia for shallow reefs? Coral Reefs 36(2): 433-444
Serrano XM, Baums IB, O’Reilly K, Smith TB, Jones RJ, Shearer TL, Nunes FLD, Baker AC (2014) Geographic differences in vertical connectivity in the Caribbean coral Montastraea cavernosa despite high levels of horizontal connectivity at shallow depths. Molecular Ecology 23: 4226-4240
Serrano XM, Baums IB, Smith TB, Jones RJ, Shearer TL, Baker AC (2016) Long-distance dispersal and vertical gene flow in the Caribbean brooding coral Porites astreoides. Scientific Reports 6: 21619
Sherman C, Nemeth M, Ruíz H, Bejarano I, Appeldoorn R, Pagán F, Scharer M, Weil E (2010) Geomorphology and benthic cover of mesophotic coral ecosystems of the upper insular slope of Southwest Puerto-Rico. Coral Reefs 29(2): 347-360
Sherman C, Schmidt W, Appeldoorn R, Hutchinson Y, Ruiz H, Nemeth M, Bejarano I, Cruz Motta JJ, Xu H (2016) Sediment dynamics and their potential influence on insular-slope mesophotic coral ecosystems. Continental Shelf Research 129: 1-9
Sherman CE, Locker SD, Webster JM, Weinstein DK (2019) Geology and geomorphology. In: Loya Y, Puglise KA, Bridge T, eds. Mesophotic coral ecosystems of the world. Springer, Cham. pp 849-878
Shlesinger T, Grinblat M, Rapuano H, Amit T, Loya Y (2018) Can mesophotic reefs replenish shallow reefs? Reduced coral reproductive performance casts a doubt. Ecology 99: 421-437
Shlesinger T, Loya Y (2019) Sexual reproduction of scleractinian corals is Mesophotic Coral Ecosystems vs. shallow reefs. In: Loya Y, Puglise KA, Bridge TCL (eds) Mesophotic coral ecosystems. Springer, Cham. pp 653-666
Sinniger F, Morita M, Harii S (2013) “Locally extinct” coral species Seriatopora hystrix found at upper mesophotic depths in Okinawa. Coral Reefs 32: 153-153
Sinniger F, Prasetia R, Yorifuji M, Bongaerts P, Harii S (2017) Seriatopora diversity preserved in upper mesophotic coral ecosystems in Southern Japan. Frontiers in Marine Sciences 4: 155
Slatkin M (2008) Linkage disequilibrium – understanding the evolutionary past and mapping the medical future. Nature Reviews Genetics 9: 477-485
Slattery M, Lesser MP (2012) Mesophotic coral reefs: a global model of community structure and function. Proceedings of the 12th International Coral Reef Symposium 1: 9-13
Slattery M, Lesser MP, Brazeau D, Stokes MD, Leichter JJ (2011) Connectivity and stability of mesophotic coral reefs. Journal of Experimental Biology and Ecology 408: 32-41
Slattery M, Moore S, Boye L, Whitney S, Woolsey A, Woolsey M (2018) The Pulley Ridge deep reef is not a stable refugia through time. Coral Reefs 37(2): 391-396
Smith TB, Glynn PW, Maté JL, Toth LT, Gyory J (2014) A depth refugium from catastrophic coral bleaching prevents regional extinction. Ecology 95(6): 1663-1673
Smith TB, Gyory J, Brandt ME, Miller WJ, Jossart J, Nemeth RS
(2016a) Caribbean mesophotic coral ecosystems are unlikely climate
change refugia. Global Change Biology 22(8): 2756-2765
Smith TB, Holstein DM, Ennis RS (2019) Disturbance in mesophotic
coral ecosystems and linkages to conservation and management. In:
Loya Y, Puglise KA, Bridge TCL (eds) Mesophotic coral ecosystems. Springer, Cham. pp 911-929
Smith TB, Maté JL, Gyori J (2016b) Thermal refuges and refugia for stony corals in the eastern tropical Pacific. In: Glynn WP, Manzello PD, Enoch CI (eds) Coral reefs of the eastern tropical Pacific: persistence and loss in a dynamic environment. Springer, Netherlands, Dordrecht. pp 501-515
Soto D, De Palmas S, Ho MJ, Denis V, Chen CA (2018) Spatial variation in the morphological traits of Pocillopora verrucosa along a depth gradient in Taiwan. PLoS ONE 13(8): e0202568
Spalding MD, Grenfell AM (1997) New estimates of global and regional coral reef areas. Coral Reefs 16(4): 225-230
Sponaugle S, Cowen RK (2019) Coral ecosystem connectivity between Pulley Ridge and the Florida Keys. In: Loya Y, Puglise KA, Bridge TCL (eds) Mesophotic coral ecosystems. Springer, Cham. pp 897-907
Starger CJ, Yeoh SSR, Dai CF, Baker AC, DeSalle R (2008) Ten polymorphic STR loci in the cosmopolitan reef coral, Pocillopora damicornis. Molecular Ecology Resources 8(3): 619-621
Stefani F, Benzoni F, Pichon M, Cancelliere C, Galli P (2008) A multidisciplinary approach to the definition of species boundaries in branching species of the coral genus Psammocora (Cnidaria, Scleractinia). Zoologica Scripta 37(1): 71-91
Studivan MS, Voss JD (2018) Population connectivity among shallow and mesophotic Montastraea cavernosa corals in the Gulf of Mexico identifies potential for refugia. Coral Reefs 37(4): 1183-1196
Thomas CJ, Bridge TCL, Figueiredo J, Deleersnijder E, Hanert E (2015) Connectivity between submerged and near-surface coral reefs: can submerged reef populations act as refuges? Diversity and Distribution 21(10): 1254-1266
Tilman D (1994) Competition and biodiversity in spatially structured habitats. Ecology 75: 2-16
Titlyanov EA, Latypov YY (1991) Light dependence in scleractinian distribution in the sublittoral zone of South China Sea Islands. Coral Reefs 10: 133-138
Titlyanov EA, Titlyanova TV, Yamazato K, Van Woesik R (2001) Photo-acclimation dynamics of the coral Stylophora pistillata to low and extremely low light. Journal of Experimental Marine Biology and Ecology 263: 211-225
Todd PA (2008) Morphological plasticity in scleractinian corals. Biological Reviews 83: 315-337
Torda G, Lundgren P, Willis BL, van Oppen MJH (2013) Genetic assignment of recruits reveals short- and long-distance larval dispersal in Pocillopora damicornis on the Great Barrier Reef. Molecular Ecology 22: 5821-5834
Torres AF, Ravago-Gotanco R (2018) Rarity of the “common” coral Pocillopora damicornis in the western Philippine archipelago. Coral Reefs 37(4): 1209-1216
Turner JA, Babcock RC, Hovey R, Kendrick GA (2017) Deep thinking: a systematic review of mesophotic coral ecosystems. ICES Journal of Marine Science 74(9): 2309-2320
van Hooidonk, Maynard JA, Planes S (2013) Temporary refugia for coral reefs in a warming world. Nature Climate Change 3: 508-511534
van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellites data. Molecular Ecology Notes 4(3): 535-538
van Oppen MJH, Bongaerts P, Underwood JN, Peplow LM, Cooper TF (2011) The role of deep reefs in shallow reef recovery: an assessment of vertical connectivity in a brooding coral from west and east Australia. Molecular Ecology 20(8): 1647-1660
van Oppen MJH, Koolmees EM, Veron JEN (2004) Patterns of evolution in the scleractinian coral genus Montipora (Acroporidae). Marine Biology 144: 9-18
van Woesik R, Houk P, Isechal AL, Idechong JW, Victor S, Golbuu Y (2012) Climate-change refugia in the sheltered bays of Palau: analogs of future reefs. Ecology and Evolution 2(10): 2474-2484
Vaz AC, Paris CB, Olascoaga MJ, Kourafalou VH, Kang H, Reed JK (2016) The perfect storm: Match-mismatch of bio-physical events drives larval reef fish connectivity between Pulley Ridge mesophotic reef and the Florida Keys. Continental Shelf Research 125: 136-146
Vega Thurber RL, Burkepile DE, Fuchs C, Shantz AA, McMinds R, Zaneveld JR (2014) Chronic nutrient enrichment increases prevalence and severity of coral disease bleaching. Global Change Biology 20(2): 544-554
Veron J (2013) Overview of the taxonomy of zooxanthellate Scleractinia. Zoological Journal of the Linnean Society 169(3): 485-508
Veron JEN (1986) Corals of Australia and the Indo-Pacific. Angus & Robertson, Sydney, Australia. 644p
Veron JEN (2000) Corals of the world. Vol 1-3. Stafford-Smith (Ed.) Australian Institute of Marine Science. Townsille, Australia. 1382p
Veron JEN (2002) New species described in Corals of the World. Australian Institute of Marine Science Monograph Series. 212p
Veron JEN, Pichon M (1976) Scleractinia of Eastern Australia. Part I. Thamnasteriidae, Astrocoeniidae, Pocilloporidae. Australian Institute of Marine Science Monograph Series. 86p
Veron JEN, Pichon M (1980) Scleractinia of Eastern Australia. Part III. Family Agariciidae, Siderastreidae, Fungiidae, Oculinidae, Merulinidae, Mussidae, Pectinidae, Caryophyllidae, Dendrophylliidae. Australian Institute of Marine Science Monograph Series. 459p
Veron JEN, Pichon M (1982) Scleractinia of Eastern Australia. Part IV. Family Poritidae. Australian Institute of Marine Science Monograph Series. 159p
Veron JEN, Pichon M, Wijsman-Best M (1977) Scleractinia of Eastern Australia. Part II. Family Faviidae, Trachyphylliidae. Australian Institute of Marine Science Monograph Series. 233p
Veron JEN, Stafford-Smith MG, DeVantier LM, Turak E (2015) Overview of distribution patterns of zooxanthellate Scleractinia. Frontiers in Marine Science 1: 81
Veron JEN, Stafford-Smith MG, Turak E, DeVantier LM (2019) Corals of the World. Accessed October 24th, 2019, version 0.01 (Beta).
Veron JEN, Wallace CC (1984) Scleractinia of Eastern Australia. Part V. Family Acroporidae. Australian Institute of Marine Science Monograph Series. 485p
Wallace CC (1999) Staghorn corals of the world: a revision of the coral
genus Acropora. CSIRO Publishing, Collingwood, Australia. 422p
Wallace CC (2012) Acroporidae of the West Atlantic. Geologica Belgica 15: 388-393
Warner RR, Cowen RK (2002) Local retention of production in marine populations: Evidence, mechanisms, and consequences. Bulletin of Marine Science 70(1): 245-249
Waters CN, Zalasiewicz J, Summerhayes C, Barnosky AD, Poirier C, Galuszka A, Cearreta A, Edgeworth M, Ellis EC, Ellis M, Jeandel C, Leinfelder R, McNeil JR, Richter DD, Steffen W, Syvitski J, Vidas D, Wagreich M, Williams M, Zhisheng A, Grinewald J, Odada E, Oreskes N, Wolfe A (2016) The Anthropocene is functionally and stratigraphically distinct from the Holocene. Science 351(6269): aad2622
Wattier R, Engel-Gautier C, Saumitou-Laprade P, Valero M (2002) Short allele dominance as a source of heterozygote deficiency at microsatellite loci: Experimental evidence at the dinucleotide locus Gv1CT in Gracilaria gracilis (Rhodophyta). Molecular Ecology 7(11) 1569-1573
White KN, Ohara T, Fujii T, Kawamura I, Mizuyama M, Montenegro J, Shikiba H, Naruse T, McClelland TY, Denis V, Reimer JD (2013) Typhoon damage on a shallow mesophotic reef in Okinawa, Japan. PeerJ 1: e151
Wild C, Hoegh-Guldberg O, Naumann MS, Colombo-Paletta MF, Atewebehan M, Fitt WK, Iglesias-Prieto R, Palmer C, Bythell JC, Ortiz JC, Loya Y, van Woesik R (2011) Climate change impedes scleractinian corals as primary reef ecosystems engineers. Marine and Freshwater Research 62(2): 205-215
Wilkinson CR (1999) Global and local threats to reef functioning and existence: reviews and predictions. Marine and Freshwater Research 50(8): 867-878
Williams GJ, Graham NAJ, Jouffray JB, Norström AV, Nyström M, Gove JM, Heenan A, Wedding L (2019) Coral reef ecology in the Anthropocene. Funtional Ecology 33(6): 1014-1022
Woodhead AJ, Hicks CC, Norström AV, Williams GJ, Graham NAJ (2019) Coral reef ecosystem services in the Anthropocene. Functional Ecology 33(6): 1023-1034
WoRMS Editorial Board (2019) World Register of Marine Species. Available from http://www.marinespecies.org at VLIZ. Accessed 2019-11-06.
Ziegler M, Roder CM, Buchel C, Voolstra CR (2014) Limits to physiological plasticity of the coral Pocillopora verrucosa from the Red Sea. Coral Reefs 33: 1115-1129