Updated May 2023.            * denotes graduate student co-authors


Crandall ED, Toczydlowski RH, Liggins L, Holmes AE, Ghoojaei M, Gaither MR,…Farrell E*, et al. (2023) The importance of timely metadata curation to the global surveillance of genetic diversity. Conservation Biology, Early View, e14061.

Cybulski JD, Skinner C, Wan Z, Wong CKM, Toonen RJ, Gaither MR, Soong K, Wyatt ASJ, Baker DM (2022) Improving stable isotope assessments of inter- and intra-species variation in coral reef fish trophic strategies. Ecology and Evolution, 12 (9), e9221.

Kumar G, Reaume A*, Farrell E*, Gaither MR (2022) Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary. PloSOne, 17 (6), e0266720. https://doi.org/10.1371/journal.pone.0266720

Toczydlowski RH, Liggins L, Gaither MR, Anderson TJ, Barton RL, Berg JT, Beskid SG, Davis B, Delgado A, Farrell E* et al. (2021) Poor data stewardship will hinder global genetic diversity surveillance. Proceedings of the National Academy of Sciences, 118(34). 

Kumar G, Farrell E*, Reaume AM*, Eble JA, Gaither MR (2021) One size does not fit all: Tuning eDNA protocols for high‐and low‐turbidity water sampling. Environmental DNA.

Liu SYV, Green J, Briggs D, Hastings R, Jondelius Y, Kensinger S, Leever H, Santos S, Throne T, Cheng C, Madduppa H, Toonen RJ, Gaither MR, Crandall ED (2021) Dongsha Atoll is an important stepping-stone that promotes regional genetic connectivity in the South China Sea. PeerJ, 9:e12063. 

Gaither MR, Coker DJ, Greaves S, Sarigol F, Payet SD, Chaidez V, Sinclair‐Taylor TH, DiBattista JD, Berumen ML (2020) Does color matter? Molecular and ecological divergence in four sympatric color morphs of a coral reef fish. Ecology and Evolution, 10 (18), 9663-9681.  

Riginos C, Crandall ED, Liggins L, Gaither MR, Ewing RB, Meyer C, Andrews KR, Euclide PT, Titus BM, Therkildsen NO (2020) Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research. Molecular Ecology Resources, 20 (6), 1458-1469.  

Klanten OS, Gaither MR, Greaves S*, Mills K, O’Keeffe K, Turnbull J, McKinnon R, Booth DJ (2020) Genomic and morphological evidence of distinct populations in the endemic common (weedy) seadragon Phyllopteryx taeniolatus (Syngnathidae) along the east coast of Australia. PloS One, 15 (12), e0243446. 

Kumar G, Eble JE, Gaither MR (2020) A practical guide to sample preservation and pre‐PCR processing of aquatic environmental DNA. Molecular Ecology Resources, 20 (1), 29-39.  

Gaither MR, Greaves S*, Amirthalingam P* (2020) The physiology of rapid ecological specialization: A look at the Midas cichlids. Molecular Ecology, 29 (7), 1216-1218.

DiBattista JD, Saenz-Agudelo P, Piatek MJ, Cagua EF, Bowen BW, Choat JH, Rocha LA, Gaither MR, Hobbs J-PA, Sinclair-Taylor TH, et al. (2020) Population genomic response to geographic gradients by widespread and endemic fishes of the Arabian Peninsula. Ecology and Evolution, 10 (10), 4314-4330.

Salas EM, Bernardi G, Berumen ML, Gaither MR, Rocha LA (2019) RADseq analyses reveal concordant Indian Ocean biogeographic and phylogeographic boundaries in the reef fish Dascyllus trimaculatus. Royal Society of Open Science 6:172413.

Crandall ED, Riginos C, Bird CE, Liggins L, Treml E, Beger M, Barber PH, Connolly SR, Cowman PF, DiBattista J, Eble JA, Magnuson SF, Horne JB, Kochzius M, Lessios HA, Liu SYV, Ludt WB, Madduppa H, Pandolfi JM, Toonen RJ, Contributing Members of the Diversity of the Indo-Pacific Network, Gaither MR (2019). The molecular biogeography of the Indo‐Pacific: Testing hypotheses with multispecies genetic patterns. Global Ecology and Biogeography. https://doi.org/10.1111/geb.12905

Crandall ED, Toonen RJ, ToBo Laboratory, & Selkoe KA (2019). A coalescent sampler successfully detects biologically meaningful population structure overlooked by F‐statistics. Evolutionary applications, 12(2), 255-265.

Gaither MR, de Jong M, Sarigol F, Neat F, Regnier T, Moore D, et al. (2018) Genomics of habitat choice and adaptive evolution in the deep-sea. Nature Ecology and Evolution, 2, 680-687.

Violi B, Gaither MR, Burns F, Hoelzel AR, Neat F. (2018) Assessing ecological and molecular divergence between the closely related ratfishes Hydrolagus pallidus and H. affinis. Journal of Fish Biology, doi.org/10.1111/jfb.13572.

Dudoit, A, Iacchei M, Coleman RR, Gaither MR, Browne WE, Bowen BW et al. (2018). The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages. PeerJ, 6, e4409.

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.

DiBattista JD, Gaither MR, Hobbs J-PA, Rocha LA, Bowen BW (2016) Angelfishes, paper tigers, and the devilish taxonomy of the Centropyge flavissima 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 lobsterPanulirus 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 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: 1111/jbi.12068.

Gaither MR, Randall JE (2013) Reclassification of the Indo-Pacific Hawkfish Cirrhitus pinnulatus (Forster). Zootaxa, 3599, 189-196.

Gaither MR, Randall JE (2012) On the validity of the Cirrhitid fish genus 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.

Molecular Ecology Cover March 2010

Molecular Ecology Cover April 2015

BMC Evolutionary Biology Cover


Eble JA, Daly-Engel TS, DiBattista JD, Koziol A, Gaither MR (2020) Marine environmental DNA: Approaches, applications, and opportunities. Advances in Marine Biology, Volume 86,141-169. 

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.

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_16189, 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, DiBattista JD (2022). Phylogeography and Population Structure. In Methods for Fish Biology, 2nd edition (eds. Midway S, Hasler C, and Chakrabarty P), Pp. 207-232. Bethesda, Maryland: The American Fisheries Society.

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.


Forsman A, Savage AE, Hoenig BD, Gaither MR (2022) DNA metabarcoding across disciplines: sequencing our way to greater understanding across scales of biological organization. Integrative and Comparative Biology, icac090.

Gaither MR, DiBattista JD, Leray M, von der Heyden S (2022) Metabarcoding the marine environment: from single species to biogeographic patterns. Environmental DNA 4 (1), 3-8.

Gaither MR (2019) Assumptions Inhibiting Progress in Comparative Biology: A book review. Copeia, 107 (2), 387-387.