[1] LaJeunesse TC, Parkinson JE, Gabrielson PW, Jeong HJ, Reimer JD, Voolstra CR, Santos SR (2018) Systematic revision of Symbiodiniaceae highlights the antiquity and diversity of coral endosymbionts. Current Biology, 28(16), 2570-2580. https://doi.org/10.1016/j.cub.2018.07.008
[2] Suggett DJ, Warner ME, Leggat W (2017) Symbiotic dinoflagellate functional diversity mediates coral survival under ecological crisis. Trends in Ecology & Evolution, 32(10), 735-745. https://doi.org/10.1016/j.tree.2017.07.013
[3] Jokiel PL, Brown EK (2004) Global warming, regional trends and inshore environmental conditions influence coral bleaching in Hawaii. Global Change Biology, 10(10), 1627-1641. https://doi.org/10.1111/j.1365-2486.2004.00836.x
[4] Baker AC, Glynn PW, Riegl B (2008) Climate change and coral reef bleaching: An ecological assessment of long-term impacts, recovery trends and future outlook. Estuarine, coastal and shelf science, 80(4), 435-471. https://doi.org/10.1016/j.ecss.2008.09.003
[5] Coffroth MA, Santos SR (2005) Genetic diversity of symbiotic dinoflagellates in the genus Symbiodinium. Protist, 156(1), 19-34. https://doi.org/10.1016/j.protis.2005.02.004
[6] Pochon X, Gates RD (2010) A new Symbiodinium clade (Dinophyceae) from soritid foraminifera in Hawai’i. Molecular phylogenetics and evolution, 56(1), 492-497. https://doi.org/10.1016/j.ympev.2010.03.040
[7] Oliver TA, Palumbi SR (2011) Do fluctuating temperature environments elevate coral thermal tolerance? Coral reefs, 30(2), 429-440. https://doi.org/10.1007/s00338-011-0721-y
[8] Varasteh T, Shokri MR, Rajabi-Maham H, Behzadi S, Hume BC (2018) Symbiodinium thermophilum symbionts in Porites harrisoni and Cyphastrea microphthalma in the northern Persian Gulf, Iran. Marine Biological Association of the United Kingdom. Journal of the Marine Biological Association of the United Kingdom, 98(8), 2067-2073. https://doi.org/10.1017/S0025315417001746
[9] Diekmann O, Olsen J, Stam W, Bak R (2003) Genetic variation within Symbiodinium clade B from the coral genus Madracis in the Caribbean (Netherlands Antilles). Coral Reefs, 22(1), 29-33. https://doi.org/10.1007/s00338-002-0273-2
[10] LaJeunesse TJMB (2002) Diversity and community structure of symbiotic dinoflagellates from Caribbean coral reefs. Marine biology, 141(2), 387-400. https://doi.org/10.1007/s00227-002-0829-2
[11] Pettay DT, Lajeunesse TC (2007) Microsatellites from clade B Symbiodinium spp. specialized for Caribbean corals in the genus Madracis. Molecular Ecology Notes, 7(6), 1271-1274. https://doi.org/10.1111/j.1471-8286.2007.01852.x
[12] Finney JC, Pettay DT, Sampayo EM, Warner ME, Oxenford HA, LaJeunesse TC (2010) The relative significance of host–habitat, depth, and geography on the ecology, endemism, and speciation of coral endosymbionts in the genus Symbiodinium. Microbial ecology, 60(1), 250-263. https://doi.org/10.1007/s00248-010-9681-y
[13] Frade PR, Englebert N, Faria J, Visser PM, Bak RPM (2008) Distribution and photobiology of Symbiodinium types in different light environments for three colour morphs of the coral Madracis pharensis: is there more to it than total irradiance?. Coral Reefs, 27(4), 913-925. https://doi.org/10.1007/s00338-008-0406-3
[14] Leão LS, Araújo LMB, Moraes LT, Assis AM (2003) Prevalência de obesidade em escolares de Salvador, Bahia. Arquivos Brasileiros de Endocrinologia & Metabologia, 47(2), 151-157. http://dx.doi.org/10.1590/S0004-27302003000200007
[15] Francini-Filho RB, Coni EO, Meirelles PM, Amado-Filho GM, Thompson FL, Pereira-Filho GH, Bastos AC, Abrantes DP, Ferreira CM, Gibran FZ, Güth AZ (2013) Dynamics of coral reef benthic assemblages of the Abrolhos Bank, eastern Brazil: inferences on natural and anthropogenic drivers. PloS one, 8(1), p.e54260. https://doi.org/10.1371/journal.pone.0054260
[16] Nunes LT, Cord I, Francini-Filho RB, Stampar SN, Pinheiro HT, Rocha LA, Floeter SR, Ferreira CE (2019) Ecology of Prognathodes obliquus, a butterflyfish endemic to mesophotic ecosystems of St. Peter and St. Paul’s Archipelago. Coral Reefs, 38(5), pp.955-960. https://doi.org/10.1007/s00338-019-01822-8
[17] Moreira APB, Tonon LAC, Cecilia do Valle PP, Alves N, Amado-Filho GM, Francini-Filho RB, Thompson FL (2014). Culturable heterotrophic bacteria associated with healthy and bleached scleractinian Madracis decactis and the fire worm Hermodice carunculata from the remote St. Peter and St. Paul Archipelago, Brazil. Current Microbiology, 68(1), 38-46. https://doi.org/10.1007/s00284-013-0435-1
[18] Magalhães GM, Amado-Filho GM, Rosa MR, de Moura RL, Brasileiro PS, De Moraes FC, Francini-Filho RB, Pereira-Filho GH (2015) Changes in benthic communities along a 0–60 m depth gradient in the remote St. Peter and St. Paul Archipelago (Mid-Atlantic Ridge, Brazil). Bulletin of Marine Science, 91(3), pp.377-396. https://doi.org/10.5343/bms.2014.1044
[19] Baker AC (2003) Flexibility and specificity in coral-algal symbiosis: diversity, ecology, and biogeography of Symbiodinium. Annual Review of Ecology, Evolution, and Systematics, 34(1), 661-689. https://doi.org/10.1146/annurev.ecolsys.34.011802.132417
[20] Picciani N, e Seiblitz IGDL, de Paiva PC, e Castro CB, Zilberberg C (2016) Geographic patterns of Symbiodinium diversity associated with the coral Mussismilia hispida (Cnidaria, Scleractinia) correlate with major reef regions in the Southwestern Atlantic Ocean. Marine biology, 163(11), 1-11. https://doi.org/10.1007/s00227-016-3010-z
[21] Silva-Lima AW, Walter JM, Garcia GD, Ramires N, Ank G, Meirelles PM, Thompson FL (2015) Multiple Symbiodinium strains are hosted by the Brazilian endemic corals Mussismilia spp. Microbial ecology, 70(2), 301-310. https://doi.org/10.1007/s00248-015-0573-z
[22] Loh WK, Loi T, Carter D, Hoegh-Guldberg O (2001) Genetic variability of the symbiotic dinoflagellates from the wide ranging coral species Seriatopora hystrix and Acropora longicyathus in the Indo-West Pacific. Marine Ecology Progress Series, 222, 97-107. https://doi.org/10.3354/meps222097
[23] Costa CF, Sassi R, Gorlach-Lira K (2008) Zooxanthellae genotypes in the coral Siderastrea stellata from coastal reefs in northeastern Brazil. Journal of Experimental Marine Biology and Ecology, 367(2), 149-152. https://doi.org/10.1016/j.jsames.2007.10.002
[24] Banaszak AT, LaJeunesse TC, Trench RK (2000) The synthesis of mycosporine-like amino acids (MAAs) by cultured, symbiotic dinoflagellates. Journal of Experimental Marine Biology and Ecology, 249(2), 219-233. https://doi.org/10.1016/S0022-0981(00)00192-1
[25] Mies M, Francini-Filho RB, Zilberberg C, Garrido AG, Longo GO, Laurentino E, Banha TN (2020) South Atlantic coral reefs are major global warming refugia and less susceptible to bleaching. Frontiers in Marine Science, 7, 514. https://doi.org/10.3389/fmars.2020.00514
[26] Monteiro JG, Costa CF, Gorlach-Lira K, Fitt WK, Stefanni SS, Sassi R, LaJeunesse TC (2013) Ecological and biogeographic implications of Siderastrea symbiotic relationship with Symbiodinium sp. C46 in Sal Island (Cape Verde, East Atlantic Ocean). Marine Biodiversity, 43(4), 261-272. https://doi.org/10.1007/s12526-013-0153-8
[27] Moreira APB, Meirelles PM, Santos EDO, Amado-Filho GM, Francini-Filho RB, Thompson CC, Thompson FL (2015) Turbulence-driven shifts in holobionts and planktonic microbial assemblages in St. Peter and St. Paul Archipelago, Mid-Atlantic Ridge, Brazil. Frontiers in microbiology, 6, 1038. https://doi.org/10.3389/fmicb.2015.01038
[28] Santos SR, Taylor DJ, Coffroth MA (2001) Genetic comparisons of freshly isolated versus cultured symbiotic dinoflagellates: implications for extrapolating to the intact symbiosis. Journal of Phycology, 37(5), 900-912. https://doi.org/10.1046/j.1529-8817.2001.00194.x
[29] Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Gu Y (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC genomics, 13(1), 1-13. https://doi.org/10.1186/1471-2164-13-341
[30] Hume BC, Smith EG, Ziegler M, Warrington HJ, Burt JA, LaJeunesse TC, Voolstra CR (2019) SymPortal: A novel analytical framework and platform for coral algal symbiont next‐generation sequencing ITS2 profiling. Molecular ecology resources, 19(4), 1063-1080. https://doi.org/10.1111/1755-0998.13004
[31] Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and environmental microbiology, 75(23), 7537-7541. https://doi.org/10.1128/AEM.01541-09
[32] Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC bioinformatics, 10(1), 1-9. https://doi.org/10.1186/1471-2105-10-421
[33] Eren AM, Morrison HG, Lescault PJ, Reveillaud J, Vineis JH, Sogin ML (2015) Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. The ISME journal, 9(4), 968-979. https://doi.org/10.1038/ismej.2014.195
[34] Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research, 32(5), 1792-1797. https://doi.org/10.1093/nar/gkh340
[35] Price MN, Dehal PS, Arkin AP (2010) FastTree 2–approximately maximum-likelihood trees for large alignments. PloS one, 5(3), e9490. https://doi.org/10.1371/journal.pone.0009490
[36] Zar JH (1999) Biostatistical analysis. Pearson Education India.
[37] Bongaerts P, Riginos C, Ridgway T, Sampayo EM, van Oppen MJ, Englebert N, Hoegh-Guldberg O (2010) Genetic divergence across habitats in the widespread coral Seriatopora hystrix and its associated Symbiodinium. PLoS one, 5(5), e10871. https://doi.org/10.1371/journal.pone.0010871
[38] Stat M, Bird CE, Pochon X, Chasqui L, Chauka LJ, Concepcion GT, Gates RD (2011) Variation in Symbiodinium ITS2 sequence assemblages among coral colonies. PloS one, 6(1), e15854. https://doi.org/10.1371/journal.pone.0015854
[39] Rodriguez-Lanetty M, Loh W, Carter D, Hoegh-Guldberg O (2001) Latitudinal variability in symbiont specificity within the widespread scleractinian coral Plesiastrea versipora. Marine Biology, 138(6), 1175. https://doi.org/10.1007/s002270100536
[40] Knowlton N, Rohwer F (2003) Multispecies microbial mutualisms on coral reefs: the host as a habitat. The american naturalist, 162(S4), S51-S62. https://www.jstor.org/stable/10.1086/378684
[41] Garren M, Walsh SM, Caccone A, Knowlton N (2006) Patterns of association between Symbiodinium and members of the Montastraea annularis species complex on spatial scales ranging from within colonies to between geographic regions. Coral Reefs, 25(4), 503-512. https://doi.org/10.1007/s00338-006-0146-1
[42] Valentin JL (2001) The Cabo Frio upwelling system, Brazil. In Coastal marine ecosystems of Latin America (pp. 97-105). Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-04482-7_8
[43] Diekmann O, Bak R, Stam W, Olsen J (2001) Molecular genetic evidence for probable reticulate speciation in the coral genus Madracis from a Caribbean fringing reef slope. Marine Biology, 139(2), 221-233. https://doi.org/10.1007/s002270100584
[44] Diekmann OE, Bak RPM, Tonk L, Stam WT, Olsen JL (2002) No habitat correlation of zooxanthellae in the coral genus Madracis on a Curaçao reef. Marine Ecology Progress Series, 227, 221-232. https://doi.org/10.3354/meps227221
[45] Teschima MM, Garrido A, Paris A, Nunes FL, Zilberberg C (2019) Biogeography of the endosymbiotic dinoflagellates (Symbiodiniaceae) community associated with the brooding coral Favia gravida in the Atlantic Ocean. PloS one, 14(3), e0213519. https://doi.org/10.1371/journal.pone.0213519
[46] Rowan R, Knowlton N, Baker A, Jara J (1997) Landscape ecology of algal symbionts creates variation in episodes of coral bleaching. Nature, 388(6639), 265-269. https://doi.org/10.1038/40843
[47] Baker AC, Starger CJ, McClanahan TR, Glynn PW (2004) Corals' adaptive response to climate change. Nature, 430(7001), 741-741. https://doi.org/10.1038/430741a
[48] Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular biology and evolution, 35(6), 1547-1549. https://doi.org/10.1093/molbev/msy096