Research & Publications

ToBo Lab Research

Our lab focuses on understanding patterns of marine biodiversity through the study of the genetics and ecology of a wide variety of marine species.

The ToBo Lab lab is shared by two PIs: Robert J. Toonen (To) and Brian Bowen (Bo).

Rob Toonen’s research focuses on the processes that influence dispersal and recruitment in coastal marine invertebrates, and the evolutionary consequences of larval developmental modes among Hawaiian coral reef species.

Brian Bowen’s research program is focused on the biogeography of marine vertebrates with a strong focus on coral reef fishes.

Publication Links:


ToBo Lab Publications by year:

(Last updated December 2017)

2017 (22 papers)

324) Schoepf, V., C.P. Jury, R.J. Toonen, & M. McCulloch (2017). Coral calcification mechanisms facilitate adaptive responses to ocean acidification. Proceedings of the Royal Society B: Biological Sciences. doi:10.1098/rspb.2017.2117

323) Lucas Moitinho-Silva, Shaun Nielsen, Amnon Amir, Antonio Gonzalez, Gail L. Ackermann, Carlo Cerrano, Carmen Astudillo-Garcia, Cole Easson, Detmer Sipkema, Fang Liu, Georg Steinert, Giorgos Kotoulas, Grace P. McCormack, Guofang Feng, James J. Bell, Jan Vicente, Johannes R. Björk, Jose M. Montoya, Julie B. Olson, Julie Reveillaud, Laura Steindler, Mari-Carmen Pineda, Maria V. Marra, Micha Ilan, Michael W. Taylor, Paraskevi Polymenakou, Patrick M. Erwin, Peter J. Schupp, Rachel L. Simister, Rob Knight, Robert W. Thacker, Rodrigo Costa, Russell T. Hill, Susanna Lopez-Legentil, Thanos Dailianis, Timothy Ravasi, Ute Hentschel, Zhiyong Li, Nicole S. Webster, Torsten Thomas; The sponge microbiome project, GigaScience, Volume 6, Issue 10, 1 October 2017, Pages 1–7,

322) Schuster A, Vargas S, Knapp I, Pomponi SA, Toonen RJ, Erpenbeck D, Woerheide G. (2017) Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model. bioRxiv doi: 10.1101/159806.

321) Capel KCC, Toonen RJ, Rachid CTCC, Creed JC, Kitahara MV, Forsman Z, Zilberberg C. (2017) Clone wars: asexual reproduction dominates in the invasive range of Tubastraea spp. (Anthozoa: Scleractinia) in the South-Atlantic Ocean. PeerJ 5:e3873.

320) Price, M.R. & R.J. Toonen (2017). Scaling Up Restoration Efforts in the Pacific Islands: A Call for Clear Management Objectives, Targeted Research to Minimize Uncertainty, and Innovative Solutions to a Wicked Problem. Pacific Science. 71(4):391-399.

319) Deck, J., M.R. Gaither, R. Ewing, C.E. Bird, N. Davies, C. Meyer, C. Riginos, R.J. Toonen & E.D. Crandall (2017). The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples. PLoS Biology. 15(8): e2002925.

318) Johnston, E.C., Z.H. Forsman, J-F Flot, S. Schmidt-Roach, J.H. Pinzón, I.S. S. Knapp & R.J. Toonen (2017) A genomic glance through the fog of plasticity and diversification in Pocillopora. Scientific Reports. 7: 5991, DOI:10.1038/s41598-017-06085-3.

317) McFadden, CS, R Haverkort-Yeh, AM Reynolds, A Halàsz, AM Quattrini, ZH Forsman, Y Benayahu & RJ Toonen (2017). Species boundaries in the absence of morphological, ecological or geographical differentiation in the Red Sea octocoral genus Ovabunda (Alcyonacea: Xeniidae). Molecular Phylogenetics and Evolution 112: 174-184.

316) Forsman, ZH, ISS Knapp, K Tisthammer, DAR Eaton, M Belcaid & RJ Toonen (2017). Coral hybridization or phenotypic variation? Genomic data reveal gene flow between Porites lobata and P. compressa. Molecular Phylogenetics and Evolution 111:132-148.

315) Puritz, J. B., C. C. Keever, J. A. Addison, S. S. Barbosa,  M. Byrne, M. W. Hart, R. K. Grosberg, and R. J. Toonen (2017). Life History Predicts Past and Present Population Connectivity in Two Sympatric Sea Stars. Nature Ecology & Evolution. 7(11):3916-3930.

314) Cros, A., R.J. Toonen, M.J. Donahue, S.A. Karl (2017) Connecting Palau’s marine protected areas: A population genetic approach to conservation. Coral Reefs. 36(3):735-748.

313) Voolstra, C.R., J. Lopez, S. Agrawal, A. Baxevanis, T. Bosch, H. Bracken-Grissom, T. Collins, K. Crandall, D. Distel, J-F Flot, G. Giriget, K. Kocot, A. Majeske, A. Riesgo, C. Schnitzler, A. Schultze, B. Swalla, D. Tagu, S. Vargas, G. Woerheide, M. Adamski, A. Antunes, M. Blaxter, J. Coddington, M. Dahl, C. Dunn, F. Ghiselli, S. Haddock, B. Misof, C. Mungal, S.J. O’Brien, T. Ravasi, M. de Freitas-Rebelo, R.J. Toonen, M. Uliano da Silva, X. Zhou (2017) Leveraging the Power of Community Cooperation to Advance Invertebrate Genomics Updates from the GIGA consortium.  Invertebrate Systematics. 31(1):1-7.

312) Christie, M.R., P. Meirmans, O. Gaggiotti, R.J. Toonen & C. White (2017). Disentangling the relative merits and disadvantages of parentage analysis and assignment tests for inferring population connectivity. ICES Journal of Marine Sciences. 74(6):1749-1762.

311) Stamoulis, K.A., A.M. Friedlander, C.G. Meyer, I. Fernandez-Silva, & R.J. Toonen (2017) Coral reef grazer-benthos dynamics complicated by invasive algae in a small marine reserve. Scientific Reports. 7:43819, doi:10.1038/srep43819.

310) Wilcox, C. L., Motomura, H., Matsunuma, M., & Bowen, B. W. (2017). Phylogeography of lionfishes (Pterois) indicate taxonomic over splitting and hybrid origin of the invasive Pterois volitansJournal of Heredity.

309) Bowen, BW, Gaither MR, DiBattista JD, Iacchei M, Andrews KR, Grant WS, Toonen RJ, Briggs JC. (2017). Comparative phylogeography of the ocean planet. Pp. 5 – 21 In Avise JC, Ayala FJ, Eds. In the Light of Evolution, Volume X: Comparative Phylogeography. Washington, DC: The National Academies Press. doi: 10.17226/23542.

308) Kahng, S., J.M. Copus, D. Wagner. (2017). Mesophotic coral ecosystems. Pp. 1 – 22 In S. Rossi (ed.) Marine Animal Forests. Springer, New York.

307) García, N. A. C., Campos, J. E., Musi, J. L. T., Forsman, Z. H., Muñoz, J. L. M., Reyes, A. M., & González, J. E. A. (2017). Comparative Molecular and Morphological Variation Analysis of Siderastrea (Anthozoa, Scleractinia) Reveals the Presence of Siderastrea stellata in the Gulf of Mexico. The Biological Bulletin232(1), 58-70.

306) DiBattista, J. D., Gaither, M. R., Hobbs, J. P. A., Rocha, L. A., & Bowen, B. W. (2017). Response to Delrieu-Trottin et al.: Hybrids, Color Variants and the Consistently Devilish Taxonomy of Pygmy Angelfishes. Journal of Heredity108(3), 337-339.

305) DiBattista, J.D., M.R. Gaither, J.-P. A. Hobbs, L.A. Rocha, B.W. Bowen. 2016. Angelfishes, paper tigers, and the devilish taxonomy of the Centropyge flavissima complex. Journal of Heredity 107:647 – 653.

304) Krysko, K.L., L.P. Nuñez, C.E. Newman, B.W. Bowen. (2017). Phylogenetics of kingsnakes, Lampropeltis getula complex (Serpentes: Colubridae), in eastern North America. Journal of Heredity 108:226 – 238.

303) DiBattista, J.D., M.R. Gaither, J.-P. A. Hobbs, P. Saenz-Agudelo, M.J. Piatek, B.W. Bowen, L.A. Rocha, J.H. Choat, J.H. McIlwain, M.A. Priest, T.H. Sinclair-Taylor, M.L. Berumen. (2017). Comparative phylogeography of reef fishes from the Gulf of Aden to the Arabian Sea reveals two cryptic lineages. Coral Reefs 36: 625 – 638.


2016 (35 papers)

302) Johnson, G.B., J. Hess, J.D. Reimer. 2016. The automated recovery timer (ART): An alternative to traditional ‘burnwire’-based subsea instrument recovery devises. SOJ Aquatic Research 1(1);1-4.

301) Fernandez-Silva I, J.E. Randall, D Golani, S.V. Bogorodsky. 2016. Mulloidichthys flavolineatus flavicaudus Fernandez-Silva & Randall (Perciformes, Mullidae), a new subspecies of goatfish from the Red Sea and Arabian Gulf. Zookeys 605: 131 – 157.

300) Wren, J.L.K., D.R. Kobayashi, Y. Jia, R.J. Toonen (2016) Modeled population connectivity across the Hawaiian Archipelago.  PLoS ONE 11(12): e0167626. doi: 10.1371/journal.pone.0167626.

299) Concepcion, GT, J Kenyon, IB Baums & RJ Toonen (2016) Genetic evidence for possible coral larval dispersal from the Northern Line Islands to the Hawaiian Archipelago. Galaxea Journal of Coral Reef Studies. 18(1):9-11.

298) Pyle, R.L., R. Boland, H. Bolick, B.W. Bowen, C.J. Bradley, C. Kane, R.K. Kosaki, R. Langston, K. Longenecker, A. Montgomery, F.A. Parrish, B.N. Popp, J. Rooney, C.M. Smith, D. Wagner, H.L. Spalding (2016) A comprehensive investigation of mesophotic coral ecosystems in the Hawaiian Archipelago. PeerJ 4:e2475  DOI 107717/peerj.2475

297) Hellberg ME, C Prada, MH Tan, ZH Forsman, IB Baums (2016) Getting a grip at the edge: recolonization and introgression in eastern Pacific Porites corals. Journal of Biogeography 43 (11): 2147-2159.

296) Cros, A., R.J. Toonen, S.W. Davies, S.A. Karl (2016) Population genetic structure between Yap and Palau for the coral Acropora hyacinthus. PeerJ. 4, e2330.

295) Veazey, L., E.C. Franklin, C. Kelley, J. Rooney, L.N. Frazer, R.J. Toonen (2016). The implementation of rare events logistic regression to predict the distribution of mesophotic hard corals across the main Hawaiian Islands. PeerJ. 4, e2189.

294) Capel, K.C.C., Migotto, A.E., Zilberberg, C., Lin, M.F., Forsman, Z., Miller, D.J. and Kitahara, M.V., 2016. Complete mitochondrial genome sequences of Atlantic representatives of the invasive Pacific coral species Tubastraea coccinea and T. tagusensis (Scleractinia, Dendrophylliidae): Implications for species identification. GeneOnline early. DOI:10.1016/j.gene.2016.05.034

293) Knapp IS, Puritz JB, Bird CE, Whitney JL, Sudek M, Forsman ZH, Toonen RJ. (2016) ezRAD- an accessible next-generation RAD sequencing protocol suitable for non-model organisms_v3.2. Life Sciences Protocol Repository. doi:10.17504/

292) Price, MR, ZH Forsman, I Knapp, RJ Toonen & MG Hadfield (2016). The complete mitochondrial genome of Achatinella sowerbyana (Gastropoda: Pulmonata: Stylommatophora).  Mitochondrial DNA, Part B: Resources. 10.1080/23802359.2016.1219631

291) Avise, J.C., B.W. Bowen, F.J. Ayala. (2016) In the light of evolution X: Comparative phylogeography. Proceedings of the National Academy of Sciences USA. 113(29):7957–7961.

290) Bowen, BW, Gaither MR, DiBattista JD, Iacchei M, Andrews KR, Grant WS, Toonen RJ, Briggs JC. Comparative phylogeography of the ocean planet. Proceedings of the National Academy of Sciences USA 113(29):7962–7969.

289) LaJeunesse TC, ZH Forsman, DC Wham (2016) An Indo-West Pacific ‘zooxanthella’ invasive to the western Atlantic finds its way to the Eastern Pacific via an introduced Caribbean coral Coral Reefs 35(2), 577-582

288) Salerno, J.L., B.W. Bowen, M.S. Rappe. Molecular biogeography of reef-associated microorganisms across the Hawaiian Archipelago. FEMS Microbiology Ecology 92: fiw109. doi: 10.1093/femsec/fiw109

287) Gaither, M.R., B.W. Bowen, L.A. Rocha, J.C. Briggs. 2016. Fishes that rule the world: circumglobal distributions revisited. Fish and Fisheries 17:664 – 679.

286) Tisthammer, K.H., Z.H. Forsman, V. Sindorf, T. Massey, C. Bielecki, & R.J. Toonen (2016). The complete mitochondrial genome of the lobe coral Porites lobata (Anthozoa: Scleractinia) sequenced using ezRAD. Mitochondrial DNA, Part B: Resources. Online early. DOI: 10.1080/23802359.2016.1157770

285) Edmunds, P.J., J.J. Leichter, E. Johnson, E. Tong & R.J. Toonen (2016). Ecological and genetic variation in reef building corals on four islands in French Polynesia. Limnology & Oceanography, 61(2):543-557.

284) Selkoe, K.A., C.C. D’Aloia, E.D. Crandall, M. Iacchei, L. Liggins, J.B. Puritz, S. von der Heyden & R.J. Toonen (2016) A decade of seascape genetics: contributions to basic and applied marine connectivity.  Marine Ecology Progress Series. (feature article) 554:1–19.

283) Hurley, K.K.C., M. Timmers, L.S. Godwin, J.M. Copus, D.J. Skillings, & R.J. Toonen (2016). An assessment of shallow and mesophotic reef brachyuran crab assemblages on the south shore of O‘ahu, Hawai‘i. Coral Reefs, 35(1):103-112.

282) Price, M.R., Z.H. Forsman, I. Knapp, M.G. Hadfield, R.J. Toonen (2016). The complete mitochondrial genome of Achatinella mustelina (Gastropoda: Pulmonata: Stylommatophora). Mitochondrial DNA, Part B: Resources. 1:183-185. DOI: 10.1080/23802359.2016.1149787

281) Waldrop E., J.P. Hobbs, J.E. Randall, J.D. DiBattista, L.A. Rocha, R.K. Kosaki, M.L. Berumen, B.W. Bowen. 2016. Phylogeography, population structure, and evolution of coral-eating butterflyfishes (Subgenus Corallochaetodon). Journal of Biogeography 43:1116-1129.

280) Ahti, A.P., R.R. Coleman, J.D. DiBattista, M.L. Berumen, L.A. Rocha, B.W. Bowen. 2016. Phylogeography of Indo-Pacific reef fishes: Sister wrasses Coris gaimard and C. cuvieri in the Red Sea, Indian Ocean, and Pacific Ocean. Journal of Biogeography 43:1103-1115.

279) Bowen, B.W. 2016. The three domains of conservation genetics: Case histories from the waters of Hawaii. Journal of Heredity 107:309-317.

278) DiBattista J.D., J. Whitney, M.T. Craig, J.-P. A. Hobbs, L.A. Rocha, K.A. Feldheim, M.L. Berumen, B.W. Bowen. Surgeons and suture zones: hybridization among four surgeonfish species in the Indo-Pacific. Molecular Phylogenetics and Evolution 101:203-215.

277) Toonen, R.J., B.W. Bowen, N Iacchei, J.C. Briggs (2016).  Marine Biogeography. Pp. 166-178 In Encyclopedia of Evolutionary Biology.  Edited by R.M. Kliman. Academic Press, Oxford.

276) Andrews, K.R., A.J. Williams, I. Fernandez-Silva, S.J. Newman, J.M. Copus, C. Wakefield, J.E. Randall, B.W. Bowen. 2016. Phylogeny of deepwater snappers (Genus Etelis) reveals a cryptic species pair in the Indo-Pacific and Pleistocene invasion of the Atlantic. Molecular Phylogenetics and Evolution 100:361-371

275) Iacchei M., M.R. Gaither, B.W. Bowen, R.J. Toonen.  2016. Predicting provincial boundaries for phyllosoma: range-wide phylogeography of the pronghorn spiny lobster Panulirus penicillatusJournal of Biogeography 43:1032-1044.

274) Selkoe, K.A., O.E. Gaggiotti, E.A. Treml, J.L.K. Wren, M.K. Donovan, Hawaii Reef Connectivity Consortium, R.J. Toonen. (2016) Conserving genetic diversity of whole communities: identifying patterns and landscape drivers.  Proceedings of the Royal Society B: Biological Sciences B 283(1829):20160354.

273) Coleman, R.R., J.A. Eble, J.D. DiBattista, L.A. Rocha, J.E. Randall, M.L. Berumen, B.W. Bowen. 2016. Regal phylogeography: range-wide survey of the marine angelfish Pygoplites diacanthus reveals evolutionary partitions between the Red Sea, Indian Ocean, and Pacific Ocean. Molecular Phylogenetics and Evolution 100:243-253.

272) Tenggardjaja, K.A., B.W. Bowen, G. Bernardi. 2016. Reef fish dispersal in the Hawaiian Archipelago: comparative phylogeography of three endemic damselfishes. Journal of Marine Biology: Article ID 3251814

271) Oyafuso, Z., R.J. Toonen, and E.C. Franklin. (2016) Temporal and spatial trends in prey composition of wahoo (Acanthocybium solandri): A diet analysis from the central North Pacific using visual and metabarcoding techniques. Journal of Fish Biology 88:1501 – 1523.

270) DiBattista, J.D., M. Roberts, A.H. Baird, F. Benzoni, J. Bouwmeester, B.W. Bowen, D. Coker, D.F. Lozano-Cortés, H. Choat, M.R. Gaither, J-P.A. Hobbs, M.T. Khalil, M. Kochzius, R.F. Myers, G. Paulay, V. Robitzch, L.A. Rocha, P. Saenz-Agudelo, E. Salas, T.H. Sinclair-Taylor, R.J. Toonen, M. Westneat, S.T. Williams & M.L. Berumen (2016).  A review of contemporary patterns of endemism in the Red Sea. Journal of Biogeography 43:423-439.

269) DiBattista, J.D., J.H. Choat, M.R. Gaither, J-P.A. Hobbs, D.F. Lozano-Cortés, R.F. Myers, G. Paulay, L.A. Rocha, R.J. Toonen, M.W. Westneat, M.L. Berumen (2016). On the origin of endemic species in the Red Sea. Journal of Biogeography 43:13-30.


2015 (16 papers)

 268) Fernandez-Silva I., J.E. Randall, R.R. Coleman, J.D. DiBattista, L.A. Rocha, J.D. Reimer, C.G. Meyer, B.W. Bowen. 2015. Yellow tails in a Red Sea: Phylogeography of the Indo-Pacific goatfish Mulloidichthys flavolineatus reveals isolation in peripheral provinces and cryptic evolutionary lineages. Journal of Biogeography 42: 2402 – 2413

267) Copus, J.M., R.L. Pyle, J.L. Earle. 2015. Neoniphon pencei, a new species of holocentrid (Teleostei: Beryciformes) from Rarotonga, Cook Islands. Biodiversity Data Journal 3: e4180.

266) Wilcox, C.L., M.A. Hixon. 2015. False positive tests for ciguatera may derail efforts to control invasive lionfish. Environmental Biology of Fishes 98:961 – 969.

265) Copus, J.M., C.A. Ka`apu-Lyons, R.L. Pyle. 2015b. Luzonichthys seaver, a new species of Anthiinae (Perciformes, Serranidae) from Pohnpei, Micronesia. Biodiversity Data Journal 3:e4902.

264) Knapp, I.S.S., Z.H. Forsman, G.J. Williams, R.J. Toonen, J.J. Bell (2015).  Origins of an invasive sponge to Palmyra Atoll (Haliclona (Soestella) caerulea), (order: Haplosclerida) are obscured by cryptic speciation.  PeerJ 3: e1170.

263) Westbrook, C., R. Ringang, S. Cantero, DAR AIS team & R.J. Toonen (2015).  Size-specific diet preferences of the collector urchin, Tripneustes gratilla, and implications for biocontrol of alien invasive algae in Hawaii.  PeerJ 3: e1235.

262) Forsman, Z. H., Page, C. A., Toonen, R. J., & Vaughan, D. (2015). Growing coral larger and faster: micro-colony-fusion as a strategy for accelerating coral cover. PeerJ 3: e1313.

261) Bahr, K.D., P.L. Jokiel & R.J. Toonen (2015).  The unnatural history of Kāne‘ohe Bay: Coral reef resilience in the face of centuries of anthropogenic impacts. PeerJ  Invited review. 3: e950.

260) DiBattista J.D., E. Waldrop, L.A. Rocha, M.T. Craig, M.L. Berumen, B.W. Bowen. 2015. Blinded by the bright: A lack of congruence between color morphs, phylogeography, and taxonomy in a cosmopolitan Indo-Pacific butterflyfish, Chaetodon auriga. Journal of Biogeography 42:1919 – 1929.

259) Forsman, Z., Wellington, G. M., Fox, G. E., & Toonen, R. J. (2015). Clues to unraveling the coral species problem: distinguishing species from geographic variation in Porites across the Pacific with molecular markers and microskeletal traits. PeerJ  3:e751.

258) DiBattista J.D., L.A. Rocha, J-P.A. Hobbs, S. He, M.A. Priest, T.H. Sinclair-Taylor, B.W. Bowen, M.L. Berumen. 2015. When biogeographic provinces collide: Hybridization of reef fishes at the crossroads of marine biogeographic provinces in the Arabian Sea. Journal of Biogeography 42:1601 – 1614.

257) Belcaid, M. & R.J. Toonen (2015).  Demystifying computer science for molecular ecologists.  Molecular Ecology Invited review, 24(11):2619–2640.

256) Gaither, M.R., M.A. Bernal, R.R. Coleman, B.W. Bowen, S.A. Jones, W.B. Simison, L.A. Rocha. 2015. Genomic signatures of geographic isolation and natural selection in coral reef fishes. Molecular Ecology 24:1543-1557.

255) Halàsz, A., A.M. Reynolds, C.S. McFadden, R.J. Toonen, Y. Benayahu (2015).  Can polyp pulsation be the key to species boundaries in the genus Ovabunda (Octocorallia: Alcyonacea: Xeniidae)?   Hydrobiologia.  759(1):95-107.

254) Eble, J.A., B.W. Bowen & G. Bernardi (2014) Phylogeography of reef fishes. Pp. 64 – 75 In C. Mora (ed.) Ecology and Conservation of Fishes on Coral Reefs. University of Hawaii Press, Honolulu

253) Chan, Y.L., D. Schanzenbach, & M.J. Hickerson (2015). Detecting concerted demographic response across community assemblages using hierarchical approximate Bayesian computation.  Molecular Biology and Evolution. 31(9):2501-2515.


2014 (22 papers)

 252) Tenggardjaja, K.A., B.W. Bowen, G. Bernardi. 2014. Vertical and horizontal connectivity in Chromis verater, an endemic damselfish found on shallow and mesophotic reefs in the Hawaiian Archipelago and Johnston Atoll. PLoS One 9: e115493.

251) Coleman R.R., M.R. Gaither, B. Kimokeo, F. Stanton, B.W. Bowen, R.J. Toonen. 2014. Large-scale introduction of the Indo-Pacific damselfish Abudefduf vaigiensis into Hawai‘i promotes genetic swamping of the endemic congener A. abdominalis. Molecular Ecology 23:5552 – 5565.

250) DiBattista J.D., J.E. Randall, S. Newman, B.W. Bowen. 2014. Round herring (genus Etrumeus) contain distinct evolutionary lineages coincident with a biogeographic barrier along Australia’s southern temperate coastline. Marine Biology 161:2465 – 2477.

249) Puritz, J.B., M.V. Matz, R.J. Toonen, J.N. Weber, D.I. Bolnick & C.E. Bird.  Demystifying the RAD fad.  Molecular Ecology. 23(24):5937-5942.

248) Selkoe, K.A., O. Gaggiotti, ToBo Laboratory, B.W. Bowen & R.J. Toonen. 2014.  Emergent Patterns of Population Genetic Structure for a Coral Reef Community. Molecular Ecology. 23(12): 3064–3079.

247) Puritz, J.B., Hollenbeck, C.M. and Gold, J.R. 2014. dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms. PeerJ. 2, p.e431.

246) Andrews, K.R., V. Moriwake, C. Wilcox, C. Kelley, E.G. Grau, B.W. Bowen (2014) Phylogeographic analyses of submesophotic snappers Etelis coruscans and Etelis “marshi” (Family Lutjanidae) reveal concordant genetic structure across the Hawaiian Archipelago.. PLoS One 9: e91665

245) Ylitalo-Ward, H.A., L. Watling & R.J. Toonen 2014.  First description of hatchlings and eggs of Octopus oliveri (Berry, 1914) (Cephalopoda: Octopodidae).  Journal of Molluscan Research 34(2): 79-83.

244) Longenecker, K., Y.L. Chan, R.J. Toonen, D.B. Carlon, T.L. Hunt, A.M. Friedlander, & E. DeMartini. (2014). Archaeological evidence of validity of fish populations on unexploited reefs as proxy targets for modern populations.  Conservation Biology.  28(5): 1322-1330.

243)  DeMartini, E.E., R.C. Langston, J.A. Eble (2014) Spawning seasonality and body sizes at sexual maturity on the bluespine unicornfish, Naso unicornis. Ichthyological Research  Online early DOI 10.1007/s10228-014-0393-z

242) Kahng, S.E., J.M. Copus, D. Wagner (2014) Recent advances in the ecology of mesophotic coral reef ecosystems (MCEs). Current Opinion in Environmental Sustainability 7: 72 – 81.

241) Gaither, M.R., J.K. Schultz, D. Bellwood, R.L. Pyle, J.D. DiBattista, L.A. Rocha & B.W. Bowen. (2014) Evolution of pygmy angelfishes: recent divergences, introgression, and the usefulness of color in taxonomy. Molecular Phylogenetics and Evolution 74:38 – 47.

240) Iacchei, M. (2014) Population genetic and phylogeographic insights into the phyllosomal odyssey.  Frontiers of Biogeography.  6.1: 29-37.

239) Szabo Z., B. Snelgrove, M.T. Craig, L.A. Rocha & B.W. Bowen (2014) Phylogeography of the Manybar Goatfish, Parupeneus multifasciatus reveals moderate structure between the Central and North Pacific and a cryptic endemic species in the Marquesas. Bulletin of Marine Science 90:493 – 512.

238) Skillings D.J., C.E. Bird, R.J. Toonen (2014)  Comparative population structure of two edible Indo-Pacific coral reef sea cucumbers (Echinodermata: Holothuroidea).  Bulletin of Marine Science 90(1): 359-378.

237) Iacchei, M., J.M. O’Malley & R.J. Toonen (2014).  After the gold rush: population structure of spiny lobsters in Hawai‘i following a fishery closure and the implications for contemporary spatial management.  Bulletin of Marine Science 90(1): 331-357.

236) Concepcion, G.T., I.B. Baums & R.J. Toonen (2014). Regional population structure of Montipora capitata across the Hawaiian archipelago.  Bulletin of Marine Science 90(1): 257-275.

235) Bowen, B.W., K. Shanker, N. Yasuda, M.C.D. Malay, S. von der Heyden, G. Paulay, L.A. Rocha, K.A. Selkoe, P.H. Barber, S.T. Williams, H.A. Lessios, E.D. Crandall, G. Bernardi, C.P. Meyer, K.E. Carpenter, R.J. Toonen (2014). Phylogeography Unplugged: Comparative geographic surveys in the genomic era.  Bulletin of Marine Science 90(1): 13-46.

234) Marti-Puig, P., Z.H. Forsman, R.D. Haverkort-Yeh, J.E. Maragos & R.J. Toonen (2014).  Extreme phenotypic polymorphism in Pocillopora across the Pacific; corallite morphology corresponds to genetic groups, while taxonomy based on colony morphology does not. Bulletin of Marine Science  90(1): 211-231.

233) Keyse, J., E.D. Crandall, R.J. Toonen, C.P. Meyer, E.A. Treml, C. Riginos (2014).  Scope of published population genetic data for Indo-Pacific marine fauna and future research opportunities.  Bulletin of Marine Science. 90(1): 47-78.

232) Beger, M., K. Selkoe, E. Treml, P.H. Barber, S. von der Heyden, E.D. Crandall, R.J. Toonen, C. Riginos (2014). Evolving coral reef conservation with genetic information. Bulletin of Marine Science. 90(1): 159-185.

231) von der Heyden, S., M. Beger, R.J. Toonen, R. Ravago-Gotanco, M.A. Juinio-Meñez, C. Fauvelot, C.E. Bird, G. Bernardi (2014). Integration of genetic data into marine conservation and management in the Indo-Pacific: a review and case studies.  Bulletin of Marine Science. 90(1): 123-158.


2013 (28 papers)

 230) Jury, C.P., F.I.M. Thomas, M.J. Atkinson, R.J. Toonen (2013) Buffer Capacity, Ecosystem Feedbacks, and Seawater Chemistry under Global Change. Water 2013, 5, 1303-1325; doi:10.3390/w5031303.

229) Bowen, B.W (2013) Testudines erectus: Beware the male sea turtle. Asian Diver 127(4):50 – 51.

228) Copus J.M. & A.C. Gibb (2013) A forceful upper jaw facilitates picking-based prey capture: Biomechanics of feeding in a butterflyfish Chaetodon trichrous. Zoology 116:336 – 347.

227) Gaither M.R. & Randall J.E. (2013) Reclassification of the Indo-Pacific Hawkfish Cirrhitus pinnulatus (Forster). Zootaxa 3599: 189-196.

226) Randall J.E. & J.D DiBattista (2013) A new species of damselfish (Pomacentridae) from the Indian Ocean. Aqua 19: 1-15.

225) Bowen, B.W., L.A. Rocha, R.J. Toonen, S.A. Karl, M.T. Craig, J.D. DiBattista, J.A. Eble, M.R. Gaither, D. Skillings & C.E. Bird (2013).  The origins of tropical marine biodiversity.  Trends in Ecology & Evolution. 28:359-366.

224) Sheppard, C.R.C., B.W. Bowen, C.A. Chen, M.T. Craig, J.A. Eble, N.N. Fitzsimmons, C.-H. Gan, M.R. Gaither, M. Gollock, S. Keshavmurthy, H. Koldewey, J.A. Mortimer, D. Obura, M. Pfeiffer, A.D. Rogers, A.L.S. Sheppard, C. Vogler, G. Worheide, M.-C. Yang, C. Yesson (2013) British Indian Ocean Territory (the Chagos Archipelago): Setting, Connections and the Marine Protected Area. Pp. 223 – 240 In C.R.C. Sheppard (ed.) Coral Reefs of the United Kingdom Overseas Territories, Springer Netherlands.

223) Leichter, J.J., A.L. Alldredge, G. Bernardi, A.J. Brooks, C.A. Carlson, R.C. Carpenter, P.J. Edmunds, M.R. Fewings, K.M. Hanson, J.L. Hench, S.J. Holbrook, C.E. Nelson, R.J. Schmitt, R.J. Toonen, L. Washburn, and A.S.J. Wyatt (2013) Biological and Physical Interactions on a Tropical Island Coral Reef: Transport and Retention Processes on Moorea, French Polynesia.  Oceanography 26(3):52–63.

222) Forsman, Z.H., E.C. Johnston, A.J. Brooks, T.C. Adam, & R.J. Toonen (2013).  Genetic Evidence for Regional Isolation of Pocillopora Corals from Moorea.  Oceanography 26(3):153–155.

221) Fernandez-Silva, I., B.N. Snelgrove & B.W. Bowen (2013) Twelve microsatellite DNA markers to resolve population structure of the Yellow-Striped Goatfish Mulloidichthys flavolineatus (family Mullidae). Conservation Genetics Resources 5:565 – 568.

220) Bird, C.E., E. Franklin, C. Smith & R.J. Toonen (2013).  Between tide and wave marks: A unifying model of physical zonation on littoral shores. PeerJ. 1:e154

219) Toonen, R.J., J.B. Puritz, Z.H. Forsman, J. Whitney, I. Fernandez-Silva, K. Andrews, & C.E. Bird.  (2013)  ezRAD: A Simplified Method for Genomic Genotyping in Non-Model Organisms.  PeerJ. 1:e203

218) Toonen, R.J., T.A. Wilhelm, S. Maxwell, D. Wagner, B.W. Bowen, C. Sheppard, S. Taei, T. Teroroko, R. Moffitt, C. Gaymer, L. Morgan, M. Lewis, A. Sheppard, J. Parks, A. Friedlander & Big Ocean Think Tank. (2013) One Size Does Not Fit All: The Emerging Frontier in Large-Scale Marine Conservation.  Marine Pollution Bulletin.  77(2013): 7-10.

217) Keever, C.C., J.B. Puritz, J.A. Addison, M. Byrne, R.K. Grosberg, R.J. Toonen & M.W. Hart (2013).  Shallow gene pools in the high intertidal: Extreme loss of genetic diversity in viviparous sea stars (Parvulastra).  Biology Letters.  9 20130551; doi:10.1098/rsbl.2013.0551

216) Briggs, J.C. & B.W. Bowen (2013) Evolutionary patterns: Marine shelf habitat. Journal of Biogeography 40:1023 – 1035. doi:10.1111/jbi.12082

215) Baums, I.B., S. Godwin, E. Franklin, D. Carlon & R.J. Toonen (2013).  Discordant population expansions in four species of coral-associated, Pacific hermit crabs (Anomura: Diogenidae) linked to habitat availability resulting from sea level change.  Journal of Biogeography. Online early, doi: 10.1111/jbi.12181

214) Iacchei, M., T. Ben-Horin, K. Selkoe, C.E. Bird, F.J. García-Rodríguez & R.J. Toonen. (2013) Combined analyses of kinship and Fst suggest potential drivers of chaotic genetic patchiness in high gene-flow populations.  Molecular Ecology. 22(13): 3476–3494.

213) Haverkort-Yeh, R.D., C.S. McFadden, Y. Benayahu, M. Berumen, A. Halász & R.J. Toonen.  (2013) A taxonomic survey of Saudi Arabian Red Sea octocorals (Cnidaria: Alcyonacea).  Marine Biodiversity. 43:279-291.

212) DiBattista, J.D., M.L. Berumen, M.R. Gaither, L.A. Rocha, J.A. Eble, J.H. Choat, M.T. Craig, D.J. Skillings & B.W. Bowen (2013) After continents divide: Comparative phylogeography of reef fishes from the Red Sea and Indian Ocean.  Journal of Biogeography 40:1170 – 1181. doi:10.1111/jbi.12068

211) Luck, D.G., Z.H. Forsman, R.J. Toonen, S.J. Leicht & S.E. Kahng.  (2013) Polyphyly and hidden species among Hawaii’s dominant mesophotic coral genera, Leptoseris and Pavona (Scleractinia: Agariciidae) PeerJ 1:e132

210) Fernandez-Silva, I., J. Whitney, B. Wainwright, K.R. Andrews, R.J. Toonen, H. Ylitalo-Ward, B.W. Bowen, E. Goetze, S.A. Karl (2013).  Microsatellites for next-generation ecologists: A post-sequencing bioinformatics pipeline. PLoS ONE. 8(2), e55990.

209) Gaither, M., G. Aeby, M. Vignon, Y. Meguro, M. Rigby, C. Runyon, R.J. Toonen, C.L. Wood, B.W. Bowen (2013).  An invasive fish and the time-lagged spread of its parasite across the Hawaiian archipelago. PLoS ONE. 8(2), e56940.

208) Andrews, KR., J.B. Puritz, W.F. Perrin, M. Oremus, L. Karczmarski, B.W. Bowen & R.J. Toonen (2013).  The evolving male: Spinner dolphin ecotypes are divergent at a Y chromosome marker but not mtDNA or autosomal markers.  Molecular Ecology.  22(9):2408–2423.

207) Barbosa, S.S., O.S. Klanten, J.B. Puritz, R.J. Toonen & M. Byrne (2013) Very fine-scale population genetic structure of sympatric asterinid sea stars with benthic and pelagic larvae: influence of mating system and dispersal potential.  Biological Journal of the Linnean Society.  108:821-833.

206) Fernandez-Silva, I. & R.J. Toonen (2013). Optimizing selection of microsatellite loci from 454 pyrosequencing via post-sequencing bioinformatic analyses.  Chapter 7 in: Kantartzi, S.K. (ed). Methods in Molecular Biology.

205) Puritz, J. & R.J. Toonen (2013). Next-generation sequencing for high-throughput molecular ecology: a step-by-step protocol for targeted multilocus genotyping by pyrosequencing. Chapter 6 in: Kantartzi, S.K. (ed). Methods in Molecular Biology.

204) Gaither, M.R., B.W. Bowen & R.J. Toonen (2013).  Population structure in the native range predicts the spread of introduced marine species. Proceedings of the Royal Society B: Biological Sciences.  280(1760):20130409

203) Farrar, C.E., Z.H. Forsman, R.D. Gates, J.C. Leong & R.J. Toonen (2013).  Observing the Coral Symbiome Using Laser Scanning Confocal Microscopy – Visualization challenge, Honorable Mention.  Science. 339(6119):518-518.


2012 (28 papers)

 202) Wilcox, C.L. (2012). It’s Time To e-Volve: Taking Responsibility for Science Communication

in a Digital Age. Biological Bulletin. 222(2), 85-87.

201) Bird, C., I. Fernandez-Silva, D. Skillings, & R.J. Toonen (2012).  Sympatric Speciation in the Post “Modern Synthesis” Era of Evolution.  Journal of Evolutionary Biology 39: 158 – 180.

200) Gaither M.R. & Randall J.E. (2012) On the validity of the Cirrhitid fish genus Itycirrhitus. Aqua 18:219-226. (200th lab paper award).

199) Stat, M., A. Baker, A. Correa, Z. Forsman, M. Huggett, X. Pochon, D. Skillings, C. Starger, R.J. Toonen, M. van Oppen & R.D Gates (2012).  Molecular delineation of species in the coral holobiont.  Advances in Marine Biology 63: 1-66.

198) Wagner, D., D. Luck & R.J. Toonen (2012). Biology and ecology of antipatharians (Cnidaria: Anthozoa: Hexacorallia). Invited review: Advances in Marine Biology. 63:67-132.

197) DiBattista, J.D., J.E. Randall, B.W. Bowen (2012) Review of the round herrings of the genus Etrumeus (Clupeidae: Dussumieriinae) of Africa, with description of two new species. Cybium  36(3), 447-460.

196) DiBattista, J.D., M.T. Craig, L.A. Rocha, K.A. Feldheim & B.W. Bowen (2012) Phylogeography of the Indo-Pacific butterflyfishes, Chaetodon meyeri and Chaetodon ornatissimus: Sister species reveal divergent evolutionary histories and discordant results from mtDNA and microsatellites. Journal of Heredity 103(5): 617-629.

195) Gaither, M.R., R.J. Toonen & B.W. Bowen (2012) Coming out of the starting blocks: Extended lag time rearranges genetic diversity in introduced marine fishes of Hawaii. Proceedings of the Royal Society B: Biological Sciences.  279(1744): 3948-3957.

194) Puritz, J.B., C.C. Keever, J.A. Addison, M. Byrne, M.W. Hart, R.K. Grosberg & R.J. Toonen (2012) Extraordinarily rapid life history divergence between Cryptasterina sea star species. Proceedings of the Royal Society, Series B  279(1744):3914-3922.

193) Puritz, J.P., R.J. Toonen (2012). Next-generation sequencing for high-throughput molecular ecology: A step-by-step protocol for targeted multilocus genotyping by pyrosequencing. In: S.K. Kantartzi (ed.) Methods in Molecular Biology. 11 pp..

192) Fernandez-Silva, I., R.J. Toonen (2012).  Less is more: Optimizing selection of microsatellite loci from 454 pyrosequencing via post-sequencing bioinformatic analyses. In: S.K. Kantartzi (ed.) Methods in Molecular Biology. 20 pp.

191) Ludt, W.B., M. Bernal, B.W. Bowen, L.A. Rocha (2012). Living in the past: Phylogeography and population histories of Indo-Pacific wrasses (Genus Halichoeres) in shallow lagoons versus outer reef slopes. PLoS One 7: e38042  doi:10.1371/journal.pone.0038042

190) Randall, J.E., J.D. DiBattista. (2012). Etrumeus makiawa, a new species of Round Herring (Clupeidae: Dussumierinae) from the Hawaiian Islands. Pacific Science  66:97 – 110.

189) Toonen, R.J. & R.K. Grosberg.  (2012).  Causes of chaos: spatial and temporal genetic heterogeneity in the intertidal anomuran crab Petrolisthes cinctipes. In: S. Koenemann, C. Held & C. Schubart (eds.) Phylogeography and Population Genetics in Crustacea.  Chapter 4, pp. 73 – 106.

188) Bird, C.E., S.A. Karl, P. Smouse & R.J. Toonen.  (2012). Detecting and Measuring Genetic Differentiation. In: S. Koenemann, C. Held & C. Schubart (eds.) Phylogeography and Population Genetics in Crustacea.  Chapter 2, pp. 31 – 55.

187) Wagner D, Montgomery AD, Waller RG & Toonen RJ (2012). Sexual reproduction of the commercially valuable Hawaiian black coral Antipathes griggi (Cnidaria: Antipatharia).  Coral Reefs 31: 795 – 806.

186) Puritz, J.B., J.A. Addison & R.J. Toonen (2012).  Next-Generation Phylogeography: A targeted approach for multilocus sequencing of non-model organisms. PLoS ONE 7(3): e34241.

185) O’Malley, J.M., J.C. Drazen, B.N. Popp, E. Gier & R.J. Toonen (2012).  Spatial Variability in Growth and Prey Availability of Lobsters in the Northwestern Hawaiian Islands.  Marine Ecology Progress Series 449:211-220.

184) Karl, S.A., R.J. Toonen, W.S. Grant, B.W. Bowen (2012). Common misconceptions in molecular ecology: Echos of the modern synthesis. Molecular Ecology (Invited) 21:4171–4189.

183) DiBattista, J.D., E. Waldrop, B.W. Bowen, J.K. Schultz, M.R. Gaither, R.L. Pyle, L.A. Rocha. Twisted sister species of Pygmy Angelfishes: Discordance between taxonomy, coloration, and phylogenetics. Coral Reefs  31(3): 839-851.

182) Forsman, Z, Kimokeo, B., C.E. Bird, C.L. Hunter & R.J. Toonen (2012). Coral farming: species-specific effects of light, water motion and artificial foods.  Journal of the Marine Biological Association of the UK. 92(4):721-729.

181) Toonen, R.J., T. Nakayama, T. Ogawa, A. Rossiter & J.C. Delbeek (2012).  Growth of cultured giant clams (Tridacna spp.) in low pH, high-nutrient seawater: species-specific effects of substrate and supplemental feeding under acidification. Journal of the Marine Biological Association of the UK. 92(4):731-740.

180) Timmers, M., C.E. Bird, D.J. Skillings, P.E. Smouse & R.J. Toonen. 2012. There’s no place like home: Crown-of-Thorns outbreaks in the Central Pacific are regionally derived and independent events.  PLoS ONE 7(2): e31159. DOI:10.1371/journal.pone.0031159173)

179) Whitney, N.M., W.D. Robbins, J.K. Schultz, B.W. Bowen, K.N. Holland. 2012. Phylogeography of the whitetip reef shark (Triaenodon obesus): a sedentary species with a broad distribution.  Journal of Biogeography 39: 1144 – 1156.

178) Daly-Engel, T.S., J.E. Randall, B.W. Bowen (2012). Is the Great Barracuda (Sphyraena barracuda) a reef fish or a pelagic fish?  The phylogeographic perspective. Marine Biology  159: 975 – 985

177) Briggs, J.C., B.W. Bowen (2012). A realignment of marine biogeographic provinces with particular reference to fish distributions. Journal of Biogeography 39:12 – 30.

176) Daly-Engel, T.S., K.D. Seraphin, K.N. Holland, J.P. Coffey, H.A. Nance, R.J. Toonen, B.W. Bowen (2012). Global phylogeography with mixed marker analysis reveals male-mediated dispersal in the endangered scalloped hammerhead shark (Sphyrna lewini). PLoS ONE 7(1): e29986. doi:10.1371/journal.pone.0029986

175) Sheppard, C., M. Ateweberhan, B.W. Bowen, P. Carr, C.A. Chen, C. Clubbe, M. T. Craig, R. Ebinghaus, J. Eble, N. FitzSimmons, M.R. Gaither, C.-H. Gan, M. Gollock, N. Guzman, N.A.J. Graham, A. Harris, R. Jones, S. Keshavmurthy, H. Koldewey, C.G. Lundin, J.A. Mortimer, D. Obura, M. Pfeiffer, A.R.G. Price, S. Purkis, P. Raines, J.W. Readman, B. Riegl, A. Rogers, M. Schleyer, M.R.D. Seaward, A.L.S. Sheppard, J. Tamelander, J.R. Turner, S. Visram, C. Vogler, S. Vogt, H. Wolschke, J. M.-C. Yang, S.-Y. Yang, C. Yesson  (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


2011 (37 papers)

174) Schultz, J.K., J.D. Baker, R.J. Toonen, A.L. Harting, B.W. Bowen. 2011. Range-wide genetic connectivity of the Hawaiian monk seal and implications for transplantation.  Conservation Biology 25:124-132.

173) Craig, M.T., F.J. Fodrie, L.G. Allen, L.A. Chartier & R.J. Toonen.  2011. Discordant Phylogeographic and Biogeographic Breaks in California Halibut.  Bulletin of Southern California Academy of Sciences.  110(3):141-151.

172) Szabo, Z., B.K. Kimokeo, R.J. Toonen & J.E. Randall. 2011. On the status of the Hawaiian seahorses Hippocampus hilonis, H. histrix, and H. fisheriMarine Biological Research. 7(7):701-709.

171) Toonen, R.J. 2011.  Book review:  Molecular approaches in natural resource conservation by DeWoody et al. Quarterly Review of Biology. 86(2):132.

170) Gaither, M.R., S.A. Jones, C. Kelley, S.J. Newman, L. Sorenson, B.W. Bowen. 2011. High connectivity in the deepwater snapper Pristipomoides filamentosus (Lutjanidae) across the Indo-Pacific with isolation of the Hawaiian Archipelago. PLoS One 6(12): e28913. doi:10.1371/journal.pone.0028913.

169) Gaither, M.R., Z. Szabó, M. Crepeau, C.J. Bird, R.J. Toonen. 2011. Preservation of corals in salt-saturated DMSO buffer is superior to ethanol for PCR experiments. Coral Reefs 30:329 – 333.

168) Randall, J.E., J.D. DiBattista, C. Wilcox. 2011. Acanthurus nigros Gunther, a valid species of surgeonfish, distinct from the Hawaiian A. nigroris Valenciennes. Pacific Science 65: 265 – 275.

167) Ebert, D.A., W.T. White, K.J. Goldman, L.J.V. Compagno, T.S. Daly-Engel, and R.D. Ward. 2011. Reevaluation and redescription of Squalus suckleyi (Girard, 1854) from the North Pacific, with comments on the Squalus acanthias subgroup (Squaliformes: Squalidae: Squalus). Zootaxa 2612:22 – 40.

166) Randall, J.E., J.D. DiBattista. Etrumeus makiawa, a new species of Round Herring (Clupeidae: Dussumierinae) from the Hawaiian Islands. Pacific Science 66:97 – 110.

165) Wagner, D., R.G. Waller & R.J. Toonen.  Sexual reproduction of Hawaiian black corals, with a review of reproductive processes within the order Antipatharia (Cnidaria: Anthozoa: Hexacorallia).  Invertebrate Biology.  130(3):211-225.

164) Selkoe, K.A. & R.J. Toonen 2011. Marine connectivity: a new look at pelagic larval duration and genetic metrics of dispersal (Review Article). Marine Ecology Progress Series. 436:291-305.

163) Bjorndal, K.A., B.W. Bowen, M. Chaloupka, L.B. Crowder, S.S. Heppell, C.M. Jones, M.E. Lutcavage, D. Policansky, A.R. Solow, and B.E. Witherington. 2011. Better science needed for restoration in the Gulf of Mexico. Science 330:437 – 438.

162) Leis, J.M., Hay, A.C., Gaither, M.R. 2011. Swimming ability and its rapid decrease at settlement in wrasse larvae (Teleostei: Labridae).  Marine Biology 158:1239 – 1246.

161) Gaither, M.R., B.W. Bowen, T.-R. Bordenave, L.A. Rocha, S.J. Newman, J.A. Gomez, L. van Herwerden, M.T. Craig. 2011. Phylogeography of the reef fish Cephalopholus argus (Epinephelidae) indicates Pleistocene isolation across the Indo-Pacific Barrier with contemporary overlap in the Coral Triangle. BMC Evolutionary Biology 11:189 doi:10.1186/1471-2148-11-189

160) Reece, J.S., B.W. Bowen, A. Larson. 2011. Long larval duration in moray eels (Muraenidae) ensures ocean-wide connectivity despite differences in adult niche breadth. Marine Ecology Progress Series 437: 269 – 277.

159) Wallace, B.P., A.D. DiMatteo, A.B. Bolten, M.Y. Chaloupka, B.J. Hutchinson, F.A. Abreu-Grobois, J.A. Mortimer, J.A. Seminoff, D. Amorocho, K.A.Bjorndal, J. Bourjea, B.W. Bowen, R. Briseño Dueñas, P. Casale, B.C. Choudhury, A. Costa, P.H. Dutton, A. Fallabrino, E.M. Finkbeiner, A. Girard, M.Girondot, M. Hamann;B.J. Hurley, M. Lopez-Mendilaharsu, M.A. Marcovaldi, J.A. Musick, R. Nel, N.J. Pilcher, S. Troëng, B. Witherington, R.B. Mast. 2011. Global conservation priorities for marine turtles. PLoS One  6(9) e24510. doi:10.1371/journal.pone.0024510

158) DiBattista J.D., Feldheim, K.A., B.W. Bowen. 2011. Microsatellite DNA markers for population genetic and hybridization analysis of two closely related surgeonfish species, Acanthurus nigricans and Acanthurus leucosternonConservation Genetic Resources  3: 159 – 162.

157) Wagner, D., X. Pochon, L. Irwin, R.J. Toonen & R.D. Gates (2011).  Azooxanthellate? Most Hawaiian black corals contain Symbiodinium.  Proceedings of the Royal Society B: Biological Sciences.  278(1710):1323-1328.

156) Kittinger, J. N., J. M. Pandolfi, J. H. Blodgett, T. L. Hunt, H. Jiang, K. Maly, L. McClenachan, J. K. Schultz, and B. A. Wilcox. 2011. Historical reconstruction reveals recovery in Hawaiian coral reefs. PLoS ONE 6(10):e25460. DOI: 10.1371/journal.pone.0025460

155) Dawson, M.N.,  P.H. Barber, L.I. González-Guzmán, R.J. Toonen, J.E. Dugan & R.K. Grosberg.  Phylogeography of Emerita analoga (Crustacea, Decapoda, Hippidae), an eastern Pacific Ocean sand crab with long-lived pelagic larvae.  Journal of Biogeography 38(8):1600–1612.

154) Cotton, C.F., R.D. Grubbs, T.S. Daly-Engel, P.D. Lynch, and J.A. Musick. 2011. Age, growth and reproduction of Squalus cf. mitsukurii from Hawaiian waters. Marine and Freshwater Research 62: 811-822

153) Bird, C.E., S.A. Karl, P Smouse & R.J. Toonen. 2011. Detecting and Measuring Genetic Differentiation.  In: S. Koenemann, C. Held & C. Schubart (eds.) Crustacean Issues: Phylogeography and Population Genetics in Crustacea.  Chapter 2, pp. 31 – 55.

152) Toonen, R.J. & R.K. Grosberg. 2011.  Causes of chaos: spatial and temporal genetic heterogeneity in the intertidal anomuran crab Petrolisthes cinctipes. In: S. Koenemann, C. Held & C. Schubart (eds.) Crustacean Issues: Phylogeography and Population Genetics in Crustacea. Chapter 4, pp. 73 – 106.

151) Work, T.M., Z.H. Forsman, Z. Szabó, T.D. Lewis, G.S. Aeby, R.J. Toonen. 2011. Inter-Specific Coral Chimerism: Genetically Distinct Multicellular Structures Associated with Tissue Loss in Montipora capitata. PLoS ONE 6(7): e22869. doi:10.1371/journal.pone.0022869.

150) Bird, C.E., B. Holland, B.W. Bowen & R.J. Toonen. 2011. Diversification of sympatric broadcast-spawning limpets (Cellana spp.) within the Hawaiian archipelago. Molecular Ecology. 20:2128-2141.

149) Bird, CE (2011) Morphological and behavioral evidence for adaptive diversification of sympatric Hawaiian limpets.  Journal of Integrative and Comparative Biology.  51:466-473.

148) Eble, J.A., R.J. Toonen, L. Sorenson, L.V. Basch, Y.P. Papastamatiou & B.W. Bowen. 2011. Escaping paradise: larval export from Hawaii in an Indo-Pacific reef fish, the Yellow Tang (Zebrasoma flavescens). Marine Ecology Progress Series. 428:245-258.

147) Toonen, R.J., K.R. Andrews, I.B. Baums, C.E. Bird, C.T. Concepcion, T.S. Daly-Engel, J.A. Eble, A. Faucci, M.R. Gaither, M. Iacchei, J.B. Puritz, J.K. Schultz, D.J. Skillings, M. Timmers, B.W. Bowen. 2011. Defining boundaries for applying ecosystem-based management: A multispecies case study of marine connectivity across the Hawaiian Archipelago. Journal of Marine Biology, Volume 2011#460173, 13 pages.

146) Skillings, D., C.E. Bird & R.J. Toonen.  2011. Gateways to Hawai‘i – genetic population structure of the tropical sea cucumber Holothuria atra. Journal of Marine Biology. Volume 2011, #783030, 16 pages.

145) Wiener, C.S., M. Rivera, R.J. Toonen, J. Leong, R.K. Kosaki, S.A. Karl, K. Keller & H. Johnson.  2011. Creating Effective Partnerships in Ecosystem Based Management: A Culture of Science and Management.  Journal of Marine Biology. Volume 2011, #241610, 8 pages.

144) Timmers, M.A., K. Andrews, C.E. Bird, M.J. deMaintenon, R.E. Brainard & R.J. Toonen,. 2011. Widespread dispersal of the crown-of-thorns sea star, Acanthaster planci, across the Hawaiian Archipelago and Johnston Atoll.  Journal of Marine Biology. Volume 2011, #934269, 10 pages.

143) Rivera, M., K. Andrews, D. Kobayashi, J. Wren, C. Kelley, G. Roderick & R.J. Toonen. 2011. Genetic analyses and simulations of larval dispersal reveal distinct populations and directional connectivity across the range of the Hawaiian Grouper (Epinephelus quernus). Journal of Marine Biology. Volume 2011, #765353, 11 pages.

142) DiBattista, J., C. Wilcox, M. Craig, L.A. Rocha & B.W. Bowen.  2011. Phylogeography of the Bluelined Surgeonfish, Acanthurus nigroris, reveals high connectivity and a cryptic endemic species in the Hawaiian Archipelago.  Journal of Marine Biology Volume 2011, #839134, 17 pages.

141) Eble, J.A., L.A. Rocha, M.T. Craig, B.W. Bowen. Not all larvae stay close to home: Insights into marine population connectivity with a focus on the Brown Surgeonfish. Journal of Marine Biology Volume 2011, Article ID 518516, 12 pp.

140) Puritz, J.B & R.J. Toonen. 2011. Coastal pollution limits pelagic larval dispersal.  Nature Communications.  2:226 DOI: 10.1038/ncomms1238, 8 pp.

139) Stat, M., C.E. Bird, X. Pochon, L. Chasqui, L.J. Chauka, G.T. Concepcion, D. Logan, M. Takabayashi, R.J. Toonen & R.D. Gates. 2011. Spatial distribution of Symbiodinium ITS2 in corals: interpretations associated with a multi-copy intra-genomically variable marker.  PLoS ONE 6(1): e15854.

138) DiBattista, J.D., K.A. Feldheim. Isolation and characterization of eight microsatellite loci in Chaetodon ornatissimus and cross-amplification in its sympatric sister species, Chaetodon meyeri.  Conservation Genetic Resources 3:159 – 162.


2010 (34 papers)

137) Forsman, Z.H., G.T.Concepcion, R.D.Haverkort, R.W.Shaw, J.E.Maragos & R.J.Toonen

Ecomorph or Endangered Coral? DNA and Microstructure Reveal Hawaiian Species Complexes: Montipora dilatata/flabellata/turgescens & M. patula/verrilli. PLoS ONE 5(12):e15021.

136) Forsman, ZH, GT Conception, RD Haverkort, RW Shaw, JE Maragos, RJ Toonen. 2010. Is Montipora dilatata an endangered coral species or an ecotype? Genes and skeletal microstructure lump seven Hawaiian species into four groups.  NOAA Tech. Rep., NOAA Fisheries Pacific Islands Region Protected Resource Division. 21 pp.

135) Baranets, V, Forsman Z, Karl S. (2010) Microsatellite loci for the plate-and-pillar coral, Porites rus. Conservation Genetics Resources

134) Polato, N.R., G.T. Concepcion, R.J. Toonen & I.B. Baums.  2010.  Isolation by distance across the Hawaiian Archipelago in the reef-building coral Porites lobataMolecular Ecology  19(21): 4661–4677.

133) Wagner, D., R.J. Toonen, Y.P. Papastamatiou, R.K. Kosaki, K.A. Gleason, G.B. McFall, R.C. Boland & R.L. Pyle 2010. New records of commercially valuable black corals (Cnidaria: Antipatharia) from the Northwestern Hawaiian Islands.  Pacific Science 65(2): 249-255.

132) Andrews, K.R., L. Karczmarski, W.W.L. Au, S. Rickards, C. Vanderlip, B.W. Bowen, E.G. Grau, and R.J. Toonen. 2010. Erratum: Rolling stones and stable homes: social structure, habitat diversity and population genetics of the Hawaiian spinner dolphin (Stenella longirostris). (Molecular Ecology (2010) 19 (732-748). Molecular Ecology 19:1755.

131) Wagner, D., R.J. Toonen, Y.P. Papastamatiou, R.K. Kosaki, K.A. Gleason, G.B. McFall, R.C. Boland & R.L. Pyle 2010. Survey of black coral species from the Northwestern Hawaiian Islands. Proceedings of the American Academy of Underwater Sciences In: NW Pollock (ed). Diving for Science 2010. Proceedings of the 29th American Academy of Underwater Sciences Symposium. Dauphin Island, AL: AAUS; In press.

130) Iacchei, M. & R.J. Toonen 2010. Caverns, compressed air, and crustacean connectivity: insights into Hawaiian spiny lobster populations. Proceedings of the American Academy of Underwater Sciences In: NW Pollock (ed). Diving for Science 2010. Proceedings of the 29th American Academy of Underwater Sciences Symposium. Dauphin Island, AL: AAUS; In press.

129) Skillings, D.J. & R.J. Toonen 2010. It’s just a flesh wound: non-lethal sampling for conservation genetics studies. Proceedings of the American Academy of Underwater Sciences In: NW Pollock (ed). Diving for Science 2010. Proceedings of the 29th American Academy of Underwater Sciences Symposium. Dauphin Island, AL: AAUS; In press.

128) Toonen, R.J., C. Bird, J. Eble, A. Faucci, G. Concepcion, K. Andrews, D.Skillings, M. Iacchei, I. Baums & B. Bowen. 2010. Where have all the larvae gone? Patterns of connectivity in the Hawaiian Archipelago. Proceedings of the American Academy of Underwater Sciences In: NW Pollock (ed). Diving for Science 2010. Proceedings of the 29th American Academy of Underwater Sciences Symposium. Dauphin Island, AL: AAUS; In press.

127) Wallace, B.P., A.D. DiMatteo, B.J. Hurley, E.M. Finkbeiner, A.B. Bolten, M.Y. Chaloupka, B.J. Hutchinson, F.A. Abreu-Grobois, D. Amorocho, K.A. Bjorndal, J. Bourjea, B.W. Bowen, R. Briceño Dueñas, P. Casale, B.C. Choudhury, A. Costa, P.H. Dutton, A. Fallabrino, A. Girard, M. Girondot, M.H. Godfrey, M. Hamann, M. López-Mendilaharsu, M.A. Marcovaldi, J.A. Mortimer, J.A. Musick, R. Nel, J.A. Seminoff, S. Troëng, B. Witherington, R.B. Mast. 2010. Regional management units for marine turtles: A novel framework for prioritizing conservation and research across multiple scales. PLoS One 5(12): e15465. doi:10.1371/journal.pone.0015465

126) Reece, J.S., B.W. Bowen, D.G. Smith, A.F. Larsen.  Molecular phylogenetics of moray eels (Murenidae) demonstrates multiple origins of a shell-crushing jaw (Gymnomuraena, Echidna) and multiple colonizations of the Atlantic Ocean.  Molecular Phylogenetics and Evolution 57: 829 – 835.

125) Craig, M.T., J. Eble, B.W. Bowen. 2010. Origins, ages, and populations histories: Comparative phylogeography of endemic Hawaiian butterflyfishes (genus Chaetodon). Journal of Biogeography 37:2125 – 2136.

124) Concepcion, G.T., N.R Polato, I.B. Baums & R.J. Toonen.  2010.  Development of microsatellite markers from four Hawaiian corals: Acropora cytherea, Fungia scutaria, Montipora capitata and Porites lobataConservation Genetics Resources 2:11-15.

123) Gaither, M.R., Z. Szabó, M. Crepeau, C.E. Bird & R. Toonen (2010).  Preservation of corals in salt-saturated DMSO buffer is superior to ethanol for PCR experiments.  Coral Reefs 30:329 – 333.

122) Bowen, B.W. 2010. Interview with John C. Briggs, recipient of the 2005 Alfred Russel Wallace Award.  Frontiers in Biogeography 2(3):78 – 80.

121) Forsman, Z.H., J.A. Martinez, J.E. Maragos & R.J. Toonen. 2010. Resurrection of Porites hawaiiensis Vaughan 1907; a Hawaiian coral obscured by small size, cryptic habitat, and confused taxonomy.  Zootaxa 2624:67-68.

120) Selkoe, K.A., J. Watson, C. White, T. Ben-Horin, M. Iacchei, S. Miterai, D. Siegel, S.D. Gaines & R.J. Toonen (2010).  Taking the chaos out of genetic patchiness: seascape genetics reveals ecological and oceanographic drivers of genetic patterns in three temperate reef species.  Molecular Ecology 19:3708-3726. (Invited Contribution to Special Issue in Landscape Genetics)

119) Wagner, D., M.R. Brugler, D.M. Opresko, S.C. France, A.D. Montgomery & R.J. Toonen 2010. Using morphometrics, in situ observations and genetic characters to distinguish among commercially valuable Hawaiian black coral species; a redescription of Antipathes grandis Verrill, 1928 (Antipatharia : Antipathidae).  Invertebrate Systematics 24:271-290.

118) White, C., J. Watson, D.A. Siegel, K.A. Selkoe, D.C. Zacherl & R.J. Toonen.  2010.  Ocean currents help explain population genetic structure.  Proceedings of the Royal Society B: Biological Sciences 277:1685-1694.

117) Schultz, J.K., A.J. Marshall, M. Pfunder.  2010. Genome-wide loss of diversity in the critically endangered Hawaiian monk seal.  Diversity 2010:863 – 880.

116) Bowen, B.W., B. Wallace. 2010. How sea turtles have weathered past climate changes. SWOT (State of the world of sea turtles) Vol. V:13-15.

115) Kahng, S.E., H. Spalding, R. Garcia, E. Brokovich, D. Wagner, E. Weil, L. Hinderstein & R.J. Toonen. 2010.  Community ecology of mesophotic coral reef ecosystems.  Coral Reefs 29:255–275.

114) National Research Council.  2010.  Sea Turtle Status and Trends:  Integrating Demography and Abundance.  National Academies Press, Washington, D.C.

113) Reece, J.S., B.W. Bowen, K. Joshi, V. Goz, A.F. Larson.  Phylogeography of two moray eels indicates high dispersal throughout the Indo-Pacific.  Journal of Heredity 101:391-402.

112) Grant, W.S., F. Lecomte, B.W. Bowen.  Biogeographical contingency and the evolution of tropical anchovies Cetengraulis from temperate Engraulis. Journal of Biogeography 37:1352 – 1362.

111) Daly-Engel, T.S., R.D. Grubbs, K. Feldheim, B.W. Bowen, and R.J. Toonen. 2010. Is multiple mating beneficial or unavoidable? Low multiple paternity and genetic diversity in the shortspine spurdog (Squalus mitsukurii). Marine Ecology Progress Series 403:255-267.

110) Gaither, M.R., R.J. Toonen, L. Sorenson, B.W. Bowen. 2010. Isolation and characterization of microsatellite markers for the Crimson Jobfish, Pristipomoides filamentosus (Lutjanidae). Conservation Genetic Resources. 2(1):169-172.

109) Barshis, D.J., J.H. Stillman, R.D. Gates, R.J. Toonen, L.W. Smith, C. Birkeland. 2010. Protein expression and genetic structure of the coral Porites lobata in an environmentally extreme Samoan back reef: does host genotype limit phenotypic plasticity?  Molecular Ecology 19:1705 – 1720.

108) McBride, R.S., C.R. Rocha, & B.W. Bowen. A new species of Elops (Elopiformes: Elopidae) from the North Atlantic Ocean. Zootaxa 2346:29-41.

107) Gaither, M., B.W. Bowen, R.J. Toonen, S. Planes, V. Messmer, J. Earle & D.R. Robertson.  2010. Genetic consequences of introducing allopatric lineages of Bluestriped Snapper (Lutjanus kasmira) to Hawaii. Molecular Ecology 19:1107-1121.

106) Gaither, M.R., R.J. Toonen, D.R. Robertson, S. Planes, and B.W. Bowen. 2010. Genetic evaluation of marine biogeographic barriers: perspectives from two widespread Indo-Pacific snappers (Lutjanus spp.). Journal of Biogeography 37:133-147.

105) Andrews, K.R., L. Karczmarski, W.W.L. Au, S. Rickards, C. Vanderlip, B.W. Bowen, E.G. Grau, and R.J. Toonen. 2010. Rolling stones and stable homes: social structure, habitat diversity and population genetics of the Hawaiian spinner dolphin (Stenella longirostris). Molecular Ecology 19:732–748.

104) Rodgers, K., P.L. Jokiel, C. Bird & E.K. Brown.  2010.  Quantifying the condition of Hawaiian coral reefs.  Aquatic Conservation: Marine and Freshwater Ecosystems.  20(1):93-105.

103) Concepcion, G., S.E. Kahng, M. Crepeau, E.C. Franklin, S. Coles & R.J. Toonen. 2010. Resolving natural ranges and marine invasions in a globally distributed octocoral (genus Carijoa).  Marine Ecology Progress Series. 401:113–127.  (100th lab paper award).


2009 (24 papers)

102) Randall J.E., J.K. Schultz. 2009. Pictichromis dinar, a new dottyback (Perciformes: Pseudochromidae) from Indonesia. Aqua, International Journal of Ichthyology 15: 169-176.

101) Keever, C., J. Sunday, J.B. Puritz, J.A. Addison, R.J. Toonen, R.K. Grosberg & M.W. Hart.  2009.  Discordant distribution of populations and genetic variation in a sea star with high dispersal potential. Evolution 63:3214 – 3227.

100) Brainard, R., R Moffitt, M Timmers, G Paulay, L Plaisance, N Knowlton, J Caley, F Fohrer, A Charette, C Meyer, R Toonen, S Godwin, J Martin, L Harris, J Geller, M Moews. 2009. Autonomous Reef Monitoring Structures (ARMS): A tool for monitoring indices of biodiversity in the Pacific Islands. 11th Pacific Science Inter-Congress, Papeete, Tahiti. 26 pp.

99) Kimokeo BK, Szabo Z, Saarman NP, Simison WB, Martin-Smith K, Barrows A, Baine M, Lourie S, Toonen RJ, Hamilton H. 2009.  Taxonomy and phylogeography of Hippocampus kuda in Hawai‘i.  Integrative and Comparative Biology. 49:E254.

98) Friedlander, A., D. Kobayashi, B. Bowen, C. Meyers, Y. Papastamatiou, E. DeMartini, F. Parrish, E. Treml, C. Currin, A. Hilting, J. Weiss, C. Kelley, R. O’Conner, M. Parke, R. Clark, R. Toonen, and L. Wedding (2009). In: Papahānaumokuākea Monument Biogeographic Assessment Report. Chapter 9. Connectivity and Integrated Ecosystem Studies. Pp. 291-330.  NOAA Technical Memorandum.

97) Randall, J.E. and L.A. Rocha. Halichoeres claudia, a new Indo-Pacific wrasse (Perciformes: Labridae), the fourth species of the H. ornatissimus complex.  Zoological Studies 48:709-718.

96) Helfman, G.S., B.B. Collette, D.E. Facey, and B.W. Bowen. 2009. The Diversity of Fishes, Second Edition.  Wiley-Blackwell, Oxford, UK

95) Weersing, K.A. & R.J. Toonen.  2009.  Population genetics, larval dispersal, and demographic connectivity in marine systems.  Marine Ecology Progress Series, Feature Article 393:1-12

94) Forsman, Z.H. & C. Birkeland.  2009.  Porites randalli: a new coral species (Scleractinia, Poritidae) from American Samoa.  Zootaxa  2244: 51-59.

93) Chan, Y.L., X. Pochon, M. Fisher, D. Wagner, G.T. Concepcion, S. Kahng, R.J. Toonen and R.D. Gates. 2009. Host genotypes and endosymbiotic dinoflagellate diversity in the coral Leptoseris sampled between 60-100 meter depths. BMC Ecology, Featured Article 9:21.

92) Randall, J.E. and L.A. Rocha.  2009. Chaetodontoplus poliourus, a new angelfish (Perciformes: Pomacanthidae) from the tropical western Pacific.  Raffles Bulletin of Zoology 57:511-520.

91) Ben-Horin, T., M. Iacchei, K. Selkoe, T. Mai & R.J. Toonen.  2009.  Characterization of eight polymorphic microsatellite loci for the California spiny lobster, Panulirus interruptus and cross-amplification in other achelate lobsters.  Conservation Genetics Resources.  1(1):193-197.

90) Erisman, B. E., M. T. Craig, and P. A. Hastings. 2009. A phylogenetic test of the size-advantage model: evolutionary changes in mating behavior influence the loss of sex change in a fish lineage. American Naturalist. 174(3):E83–E99.

89) Brown DP, Basch L, Barshis D, Forsman Z, D Fenner D, Goldberg J (2009) American Samoa’s island of giants: Massive Porites Colonies at Ta’u Island. Coral Reefs 28:735.

88) Franklin E.C., C. V. Brong, A. R. Dow, and M. T. Craig. 2009. Length-weight and length-length relationships of three endemic butterflyfish species (Chaetodontidae) from coral reefs of the Northwestern Hawaiian Islands, USA. Journal of Applied Ichthyology. 25(5):616-617.

87) Carvalho-Flho, Alfredo, C. E. L. Ferreira, and M. T. Craig. 2009. A shallow water population of Pronotogrammus martinencis (Guichenot, 1868) (Teleostei; Serranidae; Anthiinae) from south-western Atlantic, Brazil. Zootaxa. In Press.

86) Selkoe, K.A., B.H. Halpern, C. Ebert, E. Franklin, E. Selig, K. Casey, J. Bruno, R.J. Toonen. 2009. A map of cumulative impacts to a “pristine” coral reef ecosystem, the Papahānaumokuākea Marine National Monument.  Coral Reefs 28(3):635-650.

85) Nance, H.A., T.S. Daly-Engel, and P.B. Marko. 2009. New microsatellite loci for the endangered scalloped hammerhead shark, Sphyrna lewini. Molecular Ecology Resources 9:955-957.

84) Forsman, Z., D.J. Barshis, C. Hunter, and R.J. Toonen. 2009. Shape-shifting corals: Molecular markers show morphology is evolutionarily plastic in Porites. BMC Evolutionary Biology 9:45.

83) Eble, J.A., R.J. Toonen, B.W. Bowen. 2009. Endemism and dispersal: comparative phylogeography of three surgeonfishes across the Hawaiian Archipelago.  Marine Biology 156:689–698.

82) Haney, R. A., Dionne, M., Puritz, J. B., Rand, D. M.  2009. The comparative phylogeography of East Coast estuarine fishes in formerly glaciated sites:  Persistence versus Recolonization in Cyprinodon variegatus ovinus and Fundulus heteroclitus macrolepidotus.  Journal of Heredity 100:284-296.

81) Christie, M.R., J.A. Eble. 2009. Isolation and characterization of 23 microsatellite loci in the yellow tang, Zebrasoma flavescensMolecular Ecology Resources 9:544-546.

80) Wagner, D., S.E. Kahng & R.J. Toonen.  2009. Observations on the life history and feeding ecology of a specialized nudibranch predator (Phyllodesmium poindimiei), with implications for biocontrol of an invasive octocoral (Carijoa riisei) in Hawaii. Journal of Experimental Marine Biology and Ecology  372:64-74.

79) Schultz JK, Baker JD, Toonen RJ, Bowen BW. 2009. Extremely low genetic diversity in the Hawaiian monk seal (Monachus schauinslandi). Journal of Heredity 100: 25-33.


2008 (21 papers)

78) Skillings, D. 2008.  Laboratory culture of the soft-coral Carijoa riiseiJournal of Young Investigators 15 :8.

77) Randall, J.E., J.L. Earle & L.A. Rocha. 2008. Xyrichtys pastellus, a new razorfish from the southwest Pacific with discussion of the related X. sciistius and X. woodi. Aqua 14 (3-10):149-158.

76) Selkoe, K.A., B.S. Halpern & R.J. Toonen. 2008. Evaluating anthropogenic threats to the Northwestern Hawaiian Islands. Aquatic Conservation: Marine and Freshwater Ecosystems 18:1149-1165.

75) Randall, J.E., J.T Williams, L.A. Rocha. 2008.  The Indo-Pacific tetradontid fish Canthigaster coronata, a complex of three species.  Smithiana 9: 3-13.

74) Pyle, R.L., J.L. Earle, B.D. Greene. 2008. Five new species of the damselfish genus Chromis (Perciformes: Labroidei: Pomacentridae) from deep coral reefs in the tropical western Pacific.  Zootaxa 1671:3-31.

73) Bienfang P., B. Oben, S. DeFelice, P. Moeller, K. Huncik, P. Oben, R. Toonen, T. Daly-Engel, and B. Bowen. 2008. Ciguatera: Detection of Neurotoxins in Carnivorous Reef Fish from Cameroon Coast, West Africa. African Journal of Marine Science 30: 533–540.

72) Craig, M. T., R. T. Graham, , R. A. Torres, J. R. Hyde, M. O. Freitas, B. P. Ferreira, M. Hostim, L. C. Gerhardinger, A. B. Andrade, and D. R. Robertson. 2008.  How many species of goliath grouper are there? Cryptic genetic divergence in a threatened marine fish and the resurrection of a geopolitical species.  Endangered Species Research Online doi: 10.3354/esr00117

71) Rocha, L.A., K.C. Lindeman, C.R. Rocha, H.A. Lessios. 2008. Historical biogeography and speciation in the reef fish genus Haemulon (Teleostei: Haemulidae).  Molecular Phylogenetics and Evolution 48:918-928

70) White, C. & R.J. Toonen. 2008. Isolation and characterization of polymorphic COI and microsatellite loci from the whelk Kelletia kelletia. Molecular Ecology Resources 8(4):881-883.

69) Concepcion, G., M. Crepeau, S.E. Kahng & R.J. Toonen. 2008. An alternative to ITS, a hypervariable, single-copy nuclear intron in corals, and its use in detecting cryptic species within the octocoral genus Carijoa. Coral Reefs 27(2):323-336.

68) Schultz JK, Feldheim KA, Gruber SH, Ashley MA, Bowen BW. 2008. Global phylogeography and seascape ecology of the lemon sharks (Genus Negaprion). Molecular Ecology 17: 5336-5348.

67) Floeter, S.R., Rocha, L.A., Robertson, D.R., Joyeux, J.C., Smith-Vaniz, W., Barreiros, J.P., Wirtz, P., Edwards, A.J., Ferreira, C.E.L., Gasparini, J.L., Bowen, B.W., Bernardi, G.  2008. Atlantic reef fish biogeography and evolution. Journal of Biogeography 35: 22-47.

66) Craig, M. T. 2008.  The goldrim surgeonfish (Acanthurus nigricans; Acanthuridae) from Diego Garcia, Chagos Archipelago: first record for the central Indian Ocean. Zootaxa 1850:65-68.

65) Craig, M. T., J. E. Randall, M. Stein. 2008. The Fourspot Butterflyfish (Chaetodon quadrimaculatus) from the Philippines and the Solomon Islands, first records for the East Indies and Melanesia. Aqua, 14(3):159-164.

64) Baker, P., J.D. Austin, B.W. Bowen, and S.M. Baker. 2008. Range-wide population structure and history of the northern quahog (Mercenaria mercenaria) inferred from mitochondrial DNA sequence data. ICES Journal of Marine Science 65:155-163.

63) Craig, M. T. and J. E. Randall.  2008.  Two new species of the Indo-Pacific clingfish genus Discotrema Briggs (Gobiesocidae).  Copeia 2008(1):66-72.

62) Rocha, L.A. and B.W. Bowen.  2008. Speciation in coral reef fishes. Journal of Fish Biology (Invited review) 72:1101-1121.

61) Rocha, L.A., C. R. Rocha, D.R. Robertson, and B. W. Bowen. 2008. Comparative phylogeography of Atlantic reef fishes indicates both origin and accumulation of diversity in the Caribbean. BMC Evolutionary Biology 8:157

60) Theisen, T.C., B.W. Bowen, W. Lanier, and J.D. Baldwin. 2008. High connectivity on a global scale in the pelagic wahoo, Acanthocybium solandri (tuna family Scombridae). Molecular Ecology 17: 4233–4247.

59) Randall JE, Schultz JK. 2008. Cirrhitops mascarenensis, a new species of hawkfish from the Mascarene Islands, southwestern Indian Ocean. Smithiana 9: 15-20.

58) Friedlander, A., J. Maragos, R. Brainard, A. Clark, G. Aeby, B. Bowen, E. Brown, K. Chaston, J. Kenyon, C. Meyer, P. McGowan, J. Miller, A. Montgomery, R. Schchroeder, C. Smith, P. Vroom, W. Walsh, I. Williams, W. Wiltse, J. Zamzow (2008). Status of Coral Reefs in Hawaii and United States Pacific Remote Island Areas (Baker, Howland, Palmyra, Kingman, Jarvis, Johnston, Wake) in 2008.  In: Status of Coral Reefs of the World: 2008. Chapter 15, pp. 213-224.


2007 (23 papers)

57) Wares, J.P., S. Daley, R. Wetzer & R.J. Toonen 2007. An evaluation of cryptic lineages of Idotea balthica (Isopoda: Idoteidae): Morphology and microsatellites. Journal of Crustacean Biology 27: 643-648.

56) Wirtz, P., C.E.L. Ferreira, S.R. Floeter, R. Fricke, J.L. Gasparini, T. Iwamoto, L. Rocha, C.L.S. Sampaio & U.K. Schliewen. 2007.  Coastal Fishes of São Tomé and Príncipe islands, Gulf of Guinea (Eastern Atlantic Ocean)—an update. Zootaxa 1523:1-48.

55) Weaver D.C. & L.A. Rocha. 2007. A New Species of Halichoeres (Teleostei: Labridae) from the Western Gulf of Mexico. Copeia 2007: 798-807.

54) Diehl, J.M., R.J. Toonen & L. Botsford. 2007.  Spatial variability of recruitment in the sand crab Emerita analoga throughout California in relation to wind-driven currents.  Marine Ecology Progress Series.  (Feature Article) 350:1-17.

53) Craig, M. T.  2007.  Facultative cleaning by the forcepsfish, Forcipiger flavissimus (Chaetodontidae).  Copeia 2007(2):459-461.

52) Bowen, B.W., and S.A. Karl. 2007. Population genetics and phylogeography of sea turtles.  Molecular Ecology (Invited review) 16: 4886–4907.

51) Bowen, B.W. 2007. Sexual harassment by a male green turtle (Chelonia mydas).  Marine Turtle Newsletter 117:10.

50) Castro A.L.F., Stewart B.S., Wilson S.G., Hueter R.H., Meekan M.G., Motta P.J., Bowen B.W., Karl S.A.  2007. Population genetic structure of Earth’s largest fish, the whale shark (Rhincodon typus).  Molecular Ecology 16: 5183-5192.

49) Rocha, L.A., M.T. Craig, and B.W. Bowen. 2007. Phylogeography and the conservation genetics of coral reef fishes. Coral Reefs (Invited review) 26: 501-512.

48) Craig, M.T., J.A. Eble, D.R. Robertson, B.W. Bowen.  2007. High genetic connectivity across the Indian and Pacific Oceans in the reef fish Myripristis berndti (Holocentridae). Marine Ecology Progress Series 334:245-254.

47) Friedlander, A., J. Caselle,  J. Beets, C. Lowe, B.W. Bowen, T. Ogawa, K. Kelly, T. Calitri, M. Lange, and B. Anderson. 2007. Aspects of the biology, ecology, and recreational fishery for bonefish at Palmyra Atoll National Wildlife Refuge, with comparisons to other Pacific Islands. Pp. 28-56 In J.S. Ault (ed.) Biology and Management of the world tarpon and bonefish fisheries. CRC Press, Boca Raton, FL

46) Faucci, A., R.J. Toonen & M.G. Hadfield. 2007. Host shift and speciation in a coral-feeding nudibranch.  Proceedings of the Royal Society B: Biological Sciences. 274:111-119.

45) Bowen, B.W., S.A. Karl, and E. Pfeiler. 2007. Resolving evolutionary lineages and taxonomy of bonefishes (Albula spp.). Pp. 147-154 In J.S. Ault (ed.) Biology and Management of the world tarpon and bonefish fisheries. CRC Press, Boca Raton, FL

44) Wagner, D., S. Kahng & R.J. Toonen.  2007. New report of nudibranch predators of the invasive octocoral Carijoa riisei in the Hawaiian Islands.  Coral Reefs 26(2):411.

43) Toonen, R.J. & A.J. Tyre.  2007. If larvae were smart: A simple model for optimal settlement choices of competent larvae. Marine Ecology Progress Series 349:43-61.

42) Bird, C.E., B.S. Holland, B.W. Bowen & R.J. Toonen.  2007. Contrasting population structure in three endemic Hawaiian limpets (Cellana spp.) with similar life histories.  Molecular Ecology 16:3173-3186.

41) Daly-Engel, T.S., R.D. Grubbs, B.W. Bowen & R.J. Toonen.  2007.  Frequency of multiple paternity in an unfished tropical population of sandbar sharks (Carcharhinus plumbeus) and implications for management.  Canadian Journal of Fisheries and Aquatic Sciences.  64:198-204.

40) Schultz, J.K., R.L. Pyle, E. DeMartini, and B.W. Bowen. 2007. Genetic homogeneity among color morphs of the flame angelfish, Centropyge loriculus. Marine Biology 151(1):167-175

39) Bowen, B.W., W.S. Grant, Z. Hillis-Starr, D. Shaver, K.A. Bjorndal, A.B. Bolten, and A.L. Bass. 2007. The advocate and the scientist; Debating the commercial exploitation of endangered hawksbill turtles. Molecular Ecology 16:3514-3515.

38) Bowen, B.W., W.S. Grant, Z. Hillis-Starr, D. Shaver, K.A. Bjorndal, A.B. Bolten, and A.L. Bass. 2007. Mixed stock analysis reveals the migrations of juvenile hawksbill turtles (Eretmochelys imbricata) in the Caribbean Sea. Molecular Ecology 16(1):49-60

37) Craig, M.T., P.A. Hastings.  2007.  A molecular phylogeny of the groupers of the subfamily Epinephelinae (Serranidae) with a revised classification of the Epinephelini.  Ichthyological Research 54(1):1-17

36) Craig, M.T.  2007.  Preliminary observations on the life history of the white-streaked grouper, Epinephelus ongus, from Okinawa, Japan.  Ichthyological Research 54(1):81-84

35) Smith, W.L., M.T. Craig.  2007.  Casting the percomorph net widely: The importance of broad taxonomic sampling in the search for the placement of serranid and percid fishes.  Copeia 2007(1): 35-55.


2006 (19 papers)

34) Schultz JK, Randall JE. 2006. Ostorhinchus leslie, a new coral-reef cardinalfish from American Samoa. Aqua 12: 1-10.

33) Andrews, K.R., L. Karczmarski, W.W.L. Au, S.H. Rickards, C.A. Vanderlip, & R.J. Toonen.  2006.  Patterns of genetic diversity of the Hawaiian spinner dolphin (Stenella longirostris).  Atoll Research Bulletin.  No. 543: 65-73.

32) Daly-Engel, T.S., R.D. Grubbs, K. Holland, R.J. Toonen & B.W. Bowen. 2006. Assessment of multiple paternity in single litters from three species of carcharhinid sharks in Hawaii. Environmental Biology of Fishes. 76: 419-424.

31) Grant, W.S., and B.W. Bowen.  2006. Living in a tilted world: climate change and geography limit speciation in Old World anchovies (Genus Engraulis). Biological Journal of the Linnaean Society 88: 673-690.

30) Bowen, B.W., A.L. Bass, A.J. Muss, J. Carlin, and D.R. Robertson. 2006. Phylogeography of two Atlantic squirrelfishes (family Holocentridae): Exploring pelagic larval duration and population connectivity.   Marine Biology 149:899-913.

29) Duncan, K.M., A.P. Martin, B.W. Bowen, and G.H. de Couet. 2006. Global phylogeography of the scalloped hammerhead shark (Sphyrna lewini). Molecular Ecology 15:2239-2251

28) Bowen, B.W., A. Muss, L.A. Rocha, and W.S. Grant.  2006. Shallow mtDNA coalescence in Atlantic pygmy angelfishes (genus Centropyge) indicates a recent invasion from the Indian Ocean. Journal of Heredity 97:1-12.

27) Selkoe, K.A. & R.J. Toonen. 2006.  Microsatellites for Ecologists: A practical guide to using and evaluating microsatellite markers. Ecology Letters 9:615-629.

26) Wares, J., P.H. Barber, J. Ross-Ibarra, E. Sotka & R.J. Toonen. (2006) Mitochondrial DNA and Population Size.  Science 314:1388-1389.

25) Concepcion, G., M. Medina & R.J. Toonen.  (2006)  Non-coding mitochondrial loci for corals.  Molecular Ecology Notes. 6:1208–1211.

24) Baums I.B., C.B. Paris, L.M. Cherubin 2006. A bio-oceanographic filter to larval dispersal in a reef-building coral.  Limnology and Oceanography 51(5):1969-1981

23) Craig, M.T., P. Bartsch, P. Wirtz, P.C. Heemstra. 2006.  Redescription and validation of Alphestes afer as an amphi-Atlantic grouper species (Perciformes : Serranidae).  Cymbium 30(4):327-331

22) Hafner, J.C., E. Reddington, M.T. Craig. 2006. Kangaroo mice (Microdipodops megacephalus) of the Mono Basin: Phylogeography of a peripheral isolate.  Journal of Mammology 87(6):1204-1217

21) Craig, M.T., D.J. Pondella. 2006.  A survey of the fishes of the Cabrillo National Monument, San Diego, California.  California Fish and Game 92(4):172-183

20) Craig, M.T., D.J. Pondella, R.N. Lea. 2006.  New records of the flag cabrilla, Epinephelus labriformis (Serranidae : Epinephelinae), from the Pacific Coast of Baja California, Mexico, and San Diego, California, USA, with notes on the distribution of other groupers in California.  California Fish and Game 92(2):91-97

19) Craig, M.T., P.A. Hastings, D.J. Pondella, D.R. Robertson, J.A. Rosales-Casian.  2006.  Phylogeography of the flag cabrilla Epinephelus labriformis (Serranidae): implications for the biogeography of the Tropical Eastern Pacific and the early stages of speciation in a marine shore fish.  Journal of Biogeography 33(6):969-979

18) Pondella, D.J., L.G. Allen, M.T. Craig, B. Gintert.  2006.  Evaluation of eelgrass mitigation and fishery enhancement structures in San Diego Bay, California.  Bulletin of Marine Science 78(1):115-131

17) Smith-Vaniz, W.F., H.L. Jelks, L.A. Rocha.  2006.  Relevance of cryptic fishes in biodiversity assessments: A case study at Buck Island Reef National Monument, St. Croix.  Bulletin of Marine Science 79(1):17-48


2005 (8 papers)

 16) Toonen, R.J., 2005. Foundations of gregariousness in barnacles. Journal of Experimental Biology 208:1773-1774.

15) Bowen, B.W. 2005. Alfred Russell Wallace Award Recipient: John C. Briggs. International Biogeography Society Newsletter 3(1): 5-6.

14) Toonen, R.J. & C.B. Wee. 2005.  An experimental comparison of sediment-based biological filtration designs for recirculating aquarium systems.  Aquaculture  250: 244– 255.

13) Rocha, L.A., D.R. Robertson, C.R. Rocha, J.L. Van Tassell, M.T. Craig, and B.W. Bowen. 2005. Recent invasion of the tropical Atlantic by an Indo-Pacific coral reef fish. Molecular Ecology 14:3921-3928.

12) Grant, W.S., R.W. Leslie, and B.W. Bowen. 2005. Molecular genetic assessment of bipolarity in the anchovy genus Engraulis. Journal of Fish Biology 67(5):1242-1265

11) Bowen, B.W. and J. Roman. 2005. Gaia’s handmaidens: the Orlog model for conservation biology. Conservation Biology 19:1037-1043.

10) Rocha, L.A., D.R. Robertson, J. Roman, and B.W. Bowen. 2005. Ecological speciation in tropical reef fishes. Proceedings of the Royal Society of London Series B 272:573-579.

9) Bowen, B.W., A.L. Bass, L. Soares, and R.J. Toonen. 2005. Conservation implications of complex population structure: lessons from the loggerhead turtle (Caretta caretta). Molecular Ecology 14: 2389-2402.


2004 (5 papers)

8) Toonen, R.J.  2004.  Genetic evidence of multiple paternity of broods in the intertidal crab, Petrolisthes cinctipesMarine Ecology Progress Series 270:259-263.

7) Briggs, J.C., B.W. Bowen and M.A. Rex. 2004. Introduction to Biogeography of the Sea. Pp. 233-237 In Lomolino and Brown (eds.) Frontiers in Biogeography.  Sinauer Assoc., Sunderland MA.

6) Toonen, R.J., M. Locke & R.K. Grosberg. 2004. Isolation and characterization of polymorphic microsatellite loci from the Dungeness crab, Cancer magisterMolecular Ecology Notes 4(2):30-32.

5) Lecomte, F.L., W.S. Grant, J.J. Dodson, R. Rodriguez-Sanchez, and B.W. Bowen. 2004. Living with uncertainty: genetic imprints of climate shifts in East Pacific anchovy (Engraulis mordax) and sardine (Sardinops sagax). Molecular Ecology 13: 2169–2182.

4) Bowen, B.W., A.L. Bass, S.-M. Chow, M. Bostrom, K.A. Bjorndal, A.B. Bolten, T. Okuyama, B. Bolker, S. Epperly, E. LaCasella, D. Shaver, M. Dodd, S. Hopkins-Murphy, J.A. Musick, M. Swingle, K. Rankin-Baransky, W. Teas, W. Witzell, and P. Dutton. 2004. Natal homing in juvenile loggerhead turtles (Caretta caretta). Molecular Ecology 13: 3797–3808.


2003 (3 papers, ToBo Lab founded: August 2003)

3) Toonen, R.J. & S. Hughes. 2003.  Increased throughput for fragment analysis on an ABI 377 automated sequencer using a 100-lane RapidLoad membrane comb and STRand software.  Section IV, Chapter 46 in: S.M. Brown (ed.) BioComputing: Computer Tools for Biologists, Eaton Publishing, Westborough, MA. Pages 391-400.

2) Branch, L.C., A.-M. Clark, P.E. Moler, and B.W. Bowen. 2003. Habitat specificity, fragmented landscapes, and the phylogeography of three lizards in Florida scrub. Conservation Genetics 4:199-212.

1) Carlin, J.L., D.R. Robertson, and B.W. Bowen. 2003. Ancient divergences and recent connections in two tropical Atlantic reef fishes Epinephelus adscensionis and Rypticus saponaceous (Percoidei: Serranidae). Marine Biology 143: 1057–1069.