UCF Biology

Michelle Gaither

Research Area(s): marine biology, ichthyology, genomics, population genetics, deep-sea, coral reefs, eDNA


The research in my lab is centered on the evolution, ecology, and origin of biodiversity in marine fishes. We are a highly collaborative lab that employs an interdisciplinary approach combining molecular tools (genome sequencing, RADSeq, and targeted capture) with field-based studies to address one of the oldest yet still hotly debated questions in biology: how do species form and specifically what are the roles of geographic isolation, ecological differentiation, and selection in the diversification of lineages? We have a number of ongoing projects involving deep-sea grenadiers, hawkfishes and surgeonfishes with a number of other projects in the works.

Additionally, our lab is investigating the utility of eDNA as a biogeographic tool to identify patterns of biodiversity, study species distributions, and evaluate anthropogenic impacts on marine ecosystems.


  • Gaither MR, Gkafas GA, de Jong M, Sarigol F, Neat F, Regnier T, Moore D, Grӧcke DR, Hall N, Liu X, John Kenny J, Lucaci A, Hughes M, Haldenby S, Hoelzel AR. Genomics of habitat choice and adaptive evolution in the deep-sea. In review at Nature Ecology and Evolution.
  •  Gaither MR, Coker DJ, Sarigol F, Payet S, Chaidez V, Sinclair-Taylor TH, DiBattista JD, Berumen M. The early signs of speciation: Molecular and ecological divergence in four sympatric color morphs of a coral reef fish. In review at Science Advances.
  •  Violi B, Gaither MR, Burns F, Hoelzel AR, Neat F. Assessing ecological and molecular divergence between the closely related ratfishes Hydrolagus pallidus and H. affinis. In review at Journal of Fish Biology.
  • Deck J, Gaither MR, Ewing R, Bird CE, Davies N, Meyer C, Riginos C, Toonen RJ & Crandall ED (2017) The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples. PLoS Biology, 15 (8) e2002925.
  • DiBattista JD, Gaither MR, Hobbs J-PA, Rocha LA, Bowen BW (2017) Response to Delrieu-Trottin et al.: Hybrids, Color Variants and the Consistently Devilish Taxonomy of Pygmy Angelfishes. Journal of Heredity, 108, 337-339.
  • DiBattista JD, Gaither MR, Hobbs J-PA, Saenz-Agudelo P, Piatek MJ, Bowen BW, Rocha LA, Choat JH, McIlwain JH, Priest MA (2017) Comparative phylogeography of reef fishes from the Gulf of Aden to the Arabian Sea reveals two cryptic lineages. Coral Reefs, 36, 625-638.
  • Bernal MA, Gaither MR, Simison WB, Sellas A, Rocha LA (2017)  Introgression and selection lead to mito-nuclear discordance in sympatric sister-species of coral reef fishes (genus Haemulon)Molecular Ecology, 26 (2), 639-652.
  • Bowen BW, Gaither MR, Dibattista JD, Iacchei M, Andrews KR, Grant W S, Toonen RJ, Briggs JC (2016) Comparative phylogeography of the ocean planet. Proceedings of the National Academy of Sciences, 113 (29), 7962-7969.
  • Gaither MR, Bowen BW, Rocha LA, Briggs J (2016) Fishes that rule the world: circumtropical distributions revisited. Fish and Fisheries, 17, 644-679.
  • DiBattista JD, Roberts MB, Baird AH, Bouwmeester J, Bowen BW, Coker DJ, Lozano-Cortes DF, Choat H, Gaither MR, Hobbs J-PA, KhalilMT, Kochzius M, Myers RF, Paulay G, Robitzch VSN, Saenz-Agudelo P, Salas E, Sinclair-Taylor TH, Toonen RJ, Westneat MW, Williams ST, Berumen ML (2016) A review of contemporary patterns of endemism for shallow water reef fauna in the Red Sea. Journal of Biogeography, 43, 423-439.
  • DiBattista JD, Choat H, Gaither MR, Hobbs J-PA, Lozano-Cortés DF, Myers RF, Paulay G, Rocha LA, Toonen RJ, Westneat MW, Berumen ML (2016) On the origin of endemic species the Red Sea. Journal of Biogeography, 43, 45-53.
  • DiBattista JD, Gaither MR, Hobbs J-PA, Rocha LA, Bowen BW (2016) Angelfishes, paper tigers, and the devilish taxonomy of the Centropyge flavissima complex. Journal of Heredity, 107, 647-653.
  •  Meguro Y, Takahashi H, Machida Y, Shirakawa H, Gaither MR, Goto A (2016) Assortative mating and divergent male courtship behaviours between two cryptic species of nine-spined sticklebacks (genus: Pungitius). Behaviour. 153(15), 1879-1911.
  • Gaither MR, Violi B, Gray HWI, Neat F, Drazen JC, Grubbs RD, Roa-Varón A, Sutton TT, Hoelzel A (2016) Depth as a driver of evolution in the deep sea: insights from grenadiers (Gadiformes: Macrouridae) of the genus Coryphaenoides. Molecular Phylogenetics and Evolution, 104, 73-82.
  • Selkoe KA, Gaggiotti OE, Treml EA, Wren JLK, Donovan M, Bowen BW, Coleman R, Concepcion GT, Craig MT, Daly-Engel TS, DiBattista JD, Eble J, Fernandez-Silva I, Franklin E, Friedlander A, Gaither MR, Gove J, Iacchei M, Jia Y, Rivera MAJ, Rocha LA, Reece J, Skillings D, Santos SR, Szabo Z, Timmers M, Wedding L, Williams GJ, Whitney N, Toonen RJ (2016) The DNA of coral reef biodiversity: predicting and protecting genetic diversity of reef assemblages. Proceedings of the Royal Society B, 283 (1829), 20160354.
  • Iacchei M, Gaither MR, Bowen BW, Toonen RJ (2016) Testing provincial boundaries for phyllosoma: Rangewide phylogeography of the pronghorn spiny lobster Panulirus penicillatus. Journal of Biogeography, 43(5), 1032-1044.
  • Saenz-Agudelo P, DiBattita JD, Piatek MJ, Gaither MR, Harrison HB, Nanninga GB, Berumen ML (2015) Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes. Molecular Ecology, 24, 6241-6255.
  •  Gaither MR, Bernal MA, Coleman R, Bowen BW, Jones SA, Simison WB, Rocha LA (2015) Genomic signatures of geographic isolation vs. natural selection in coral reef fishes. Molecular Ecology, 7, 1543-1557.
  • Gaither MR, Bernal MA, Fernandez-Silva I, Mwale M, Jones SA, Rocha C, Rocha LA (2015) Two deep evolutionary lineages in the circumglobal Glasseye, Heteropriacanthus cruentatus (Teleostei, Priacanthidae) with admixture in the Western Indian Ocean. Journal of Fish Biology, 87, 715-727.
  • Leis JM, Meyer O, Hay AC, Gaither MR (2015) A coral-reef fish with large, fast, conspicuous larvae and small, cryptic adults (Teleostei: Apogonidae). Copeia, 103, 78-86.
  • Bernal MA, Sinai NL, Rocha C, Gaither MR, Dunker F, Rocha LA (2015) Long-term sperm storage in the Brown banded Bamboo Shark Chiloscyllium punctatum. Journal of Fish Biology, 86, 1171-1176.
  • Bernal MA, Floeter SR, Gaither MR, Longo GO, Morais R, Ferreira CEL, Vermeij MJA, Rocha LA (2015) High prevalence of ecto-parasites among coral reef fishes of Curacao. Marine Biodiversity, doi: 10.1007/s12526-015-0322-z.
  • Gaither MR, Wagner D (2015) Promiscuous associations: observations of gold-saddle goatfishes in the Chagos Archipelago (Indian Ocean). Bulletin of Marine Science, 91, 321-322.
  • Coleman RR, Gaither MR, Bowen BW, Kimokeo B, Staton F, Toonen, RJ (2014) Large-scale introduction of the Indo-Pacific damselfish Abudefduf viagiensis into Hawai‘i promotes genetic swamping of the endemic congener A. abdominalis through introgression. Molecular Ecology, 23, 5552-5565.
  • Selkoe KA, Gaggiotti OE, Andrews K, Bernal MA, Bird C, Bolick H, Baums I, Coleman R, Concepcion GT, Craig MT, DiBattista JD, Eble J, Fernandez-Silva I, Gaither MR, Iacchei M, Polato, Nicholas R, Rivera MAJ, Rocha LA, Skillings D, Timmers M, Szabo Z, Bowen BW, Toonen RJ (2014) Emergent patterns of population genetic structure for a coral reef community. Molecular Ecology, 23, 3064-79.
  • Gaither MR, Schultz JK, Pyle R, Rocha LA, Bellwood D, Bowen BW (2014) The evolutionary history and phylogeny of pygmy angelfishes (Genus Centropyge). Molecular Phylogenetics and Evolution, 74, 38–47.
  • Laptikhovsky V, Gaither MR, Black A (2013) A Pacific grenadier Coryphaenoides acrolepis in the South-west Atlantic and environmental changes in the Falkland deep seas. Marine Biodiversity Records, 6, doi:10.1017/S1755267213001061.
  • Gaither MR, Bowen BW, Toonen RJ (2013) Population structure in the native range predicts the spread of introduced marine species. Proceedings of the Royal Society of London: B, 280: 20130409. http://dx.doi.org/10.1098/rspb.2013.0409.
  • Gaither MR, Aeby G, Vignon M, Meguro YI, Rigby M, Runyon C, Toonen RJ, Wood CL, Bowen BW (2013) An invasive fish and the time-lagged spread of its parasite across the Hawaiian Archipelago. PLoS One, doi: 10.1371/journal.pone.0056940.
  • DiBattista JD, Berumen ML, Gaither MR, Rocha LA, Eble JA, Choat JH, Craig MT, Skillings DJ, Bowen BW (2013) After continents divide: comparative phylogeography of reef fishes from the Red Sea and Indian Ocean. Journal of Biogeography, doi: 10.1111/jbi.12068.
  • Gaither MR, Randall JE (2013) Reclassification of the Indo-Pacific Hawkfish Cirrhitus pinnulatus (Forster). Zootaxa, 3599, 189-196.
  • Gaither MR, Rocha LA (2013) Origins of species richness in the Indo-Pacific biodiversity hotspot: evidence for the Center of Overlap hypothesis. Journal of Biogeography, 40, 1638-1648.
  • Rocha, LA, Bernal MA, Gaither MR, Alfaro M (2013) Massive Parallel Sequencing: applications for Biogeography. Frontiers in Biogeography, 5(1), fb_6189, http://www.escholarship.org/uc/item/7xv39142.
  • Bowen BW, Rocha LA, Toonen RJ, Karl SA, Craig MT, DiBattista JD, Eble JA, Gaither MR, Skillings D, Bird CJ (2013) Origins of tropical marine biodiversity. Trends in Ecology and Evolution, 28, 359-366.
  • Sheppard CR, Ateweberhan M, Bowen BW, Carr P, Chen CA, Clubbe C, Craig MT, Ebinghaus R, Eble J, Fitzsimmons N, Gaither MR, Gan CH, Gollock M, Guzman N, Graham NA, Harris AR, Keshavmurthy S, Koldewey H, Lundin CG, Mortimer JA, Obura D, Pfeiffer M, Price AR, Purkis S, Raines P, Readman JW, Riegl B, Rogers A, Schleyer M, Seaward MR, Sheppard AL, Tamelander J, Turner JR, Visram S, Vogler C, Vogt S, Wolschke H, Yang JM, Yang SY, Yesson C (2012) Reefs and islands of the Chagos Archipelago, Indian Ocean: why it is the world’s largest no-take marine protected area. Aquatic Conservation: marine and freshwater ecosystems, 22, 232-261.
  • Gaither MR, Randall JE (2012) On the validity of the Cirrhitid fish genus Itycirrhitus. Aqua: International Journal of Ichthyology, 18, 219-226.
  • Gaither MR, Toonen RJ, Bowen BW (2012) Coming out of the starting blocks: Extended lag time rearranges genetic diversity in introduced marine fishes of Hawaiʻi. Proceedings of the Royal Society of London: B,doi: 101098/rspb.2012.1481.
  • DiBattista JD, Waldrop E, Bowen BW, Schultz JK, Gaither MR, Pyle RL, Rocha LA (2012) Twisted sister species of Pygmy Angelfishes: discordance between taxonomy, coloration, and phylogenetics. Coral Reefs, 31, 839-851.
  • Gaither MR, Jones SA, Kelley C, Newman SJ, Sorenson L, Bowen BW (2011) High connectivity in the deepwater snapper Pristipomoides filamentosus (Lutjanidae) across the Indo-Pacific with isolation of the Hawaiian Archipelago. PLoS ONE, 6, doi: 10.1371/journal.pone.0028913.
  • Gaither MR, Bowen BW, Bordenave T, Rocha LA, Newman SJ, Gomez JA, van Herwerden L, Craig MT (2011) Phylogeography of the reef fish Cephalopholis argus (Epinephelidae) indicates Pleistocene isolation across the Indo-Pacific Barrier with contemporary overlap in the Coral Triangle. BMC Evolutionary Biology, 11, 189.
  • Gaither MR, Szabo Z, Crepeau M, Bird C, Toonen RJ (2011) Preservation of corals in salt-saturated DMSO/EDTA buffer (SSD) is superior to ethanol for PCR experiments. Coral Reefs, 30, 329-333.
  • Toonen RJ, Andrews KR, Baums IB, Bird CE, Concepcion GT, Daly-Engel TS, Eble JA, Faucci A, Gaither MR, Iacchei M, Puritz JB, Schultz JK, Skillings DJ, Timmers M, Bowen BW (2011) Defining boundaries for ecosystem-based management: A multispecies case study of marine connectivity across the Hawaiian Archipelago. Journal of Marine Biology, doi: 10.1155/2011/460173.
  • Leis JM, Hay AC, Gaither MR (2011) Swimming ability and its rapid decrease at settlement in wrasse larvae (Teleostei: Labridae). Marine Biology, 158, 1239-1246.
  • Gaither MR, Bowen BW, Toonen RJ, Planes S, Messmer V, Earle J, Robertson DR (2010) Genetic consequences of introducing two allopatric lineages of Bluestripe Snapper (Lutjanus kasmira) to Hawai‘i. Molecular Ecology, 19, 1107-1121.
  • Gaither MR, Toonen RJ, Robertson DR, Planes S, Bowen BW (2010) Genetic evaluation of marine biogeographic barriers: Perspectives from two widespread Indo-Pacific snappers (Lutjanus kasmira and Lutjanus fulvus). Journal of Biogeography, 37, 133-147.
  • Gaither MR, Toonen RJ, Sorenson L, Bowen BW (2010) Isolation and characterization of microsatellite markers for the Crimson Jobfish, Pristipomoides filamentosus (Lutjanidae). Conservation Genetics Resources, 2, 169-172.
  • Gaither MR, Rowan R (2010) The planular symbiosis in Pocillopora damicornis. Journal of Experimental Marine Biology and Ecology, 386, 45-53.


  • Bowen BW, Gaither MR, Dibattista JD, Iacchei M, Andrews KR, Grant W S, Toonen RJ, Briggs JC (2017) Comparative phylogeography of the ocean planet. In In the Light of Evolution, Volume X: Comparative Phylogeography (eds. Avise JC, Ayala FJ), Pp. 5 – 21. Washington, DC: The National Academies Press. doi: 10.17226/23542.
  • Sheppard CRC, Bowen BW, Chen CA, Craig MT, Eble J, Fitzsimmons N, Gaither MR, Gollock M, Keshavmurthy S, Koldewey H, Mortimer JA, Obura D, Pfeiffer M, Rogers AD, Sheppard ALS, Vogler C, Wörheide G, Yang M-C, Yesson C (2013) British Indian Ocean Territory (the Chagos Archipelago): setting, connections and the marine protected area. In Coral Reefs of the United Kingdom Overseas Territories (eds. Rigel BM, Purkis SJ), Springer Netherlands, Heidelberg.



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