The Moore Lab at FAU

Selected Publications

Ecology of Deep-sea Fishes

Gulf of Mexico References

Cook, A. B., A.M. Bernard, K.M. Boswell, H. Bracken-Grissom, S. deRada, D. English, R. Eytan, T.M. Frank, C. Hu, M. Johnston, H.L. Judkins, C. Lembke, R. Milligan, J.A. Moore, B. Penta, N. Pruzinsky, J. Quinlan, T. Richards, I.C. Romero, M. Vecchione, M. Weber, T.T. Sutton. 2020. A multidisciplinary approach to investigate pelagic ecosystem dynamics in the Gulf of Mexico, a high-diversity oceanic system subjected to large-scale industrial disturbance. Frontiers in Marine Science 7: 1-13. Available at: Front Mar Sci.

Moore, J. A., D. B. Fenolio, T. T. Sutton, and A. B. Cook. 2020. Hiding in plain sight: elopomorph larvae Are important contributors to fish biodiversity in a low-latitude oceanic ecosystem.” Frontiers in Marine Science 7: 1–13. Available at: Front Mar Sci.

Polidoro, B., Matson, C. W., Ottinger, M. A., Renegar, D. A., Romero, I. C., Schlenk, D., Wise, J. P., Sr., Gonzalez, J. B., Bruns, P., Carpenter, K., Coiban Rojas, D., Collier, T. K., Duda, T. F., Jr., Gonzalez-Diaz, P., Di Giulio, R., Grubbs, R. D., Haney, J.C., Incardona, J.P., Horta-Puga, G., Linardich, C., Moore, J. A., Pech, D., Valderrama, S. P., Ralph, G. M., Strongin, K., Ringwood, A. H., and Wursig, B. 2021. A multi-taxonomic framework for assessing relative petrochemical vulnerability of marine biodiversity in the Gulf of Mexico. Science of the Total Environment 763: 142986. Available at: Sci Total Environ.

Sutton, T. T., R.J. Milligan, K. Daly, K.M. Boswell, A.B. Cook, M. Cornic, T.M. Frank, K. Frasier, D. Hahn, F. Hernandez, J. Hildebrand, C. Hu, M. Johnston, S.B. Joye, H.L. Judkins, J.A. Moore, S.A. Murawski, M. N. Pruzinsky, J. Quinlan, A. Remsen, K. Robinson, I.C. Romero, J. Rooker, M. Vecchione, D. Wells. 2022. The open-ocean Gulf of Mexico after Deepwater Horizon: Synthesis of a Decade of Research. Frontiers in Marine Science 9: 753391. Available at: Front Mar Sci.

Woodstock, M. S., C. Golightly, D. B. Fenolio, and J. A. Moore. 2019. Larsonia pterophylla (Cnidaria, Pandeidae) parasitic on two leptocephali: Paraconger sp. (Congridae) and Callechelyini gen. sp. (Ophichthidae) in the Gulf of Mexico. Gulf and Caribbean Research 30, no. 1/5: SC7–10. Available at: Gulf Caribb Res.

Woodyard, M., B. A. Polidoro, C. W. Matson, R. A. McManamay, S. Saul, K. E. Carpenter, T K. Collier, R. Di Giulio, R. D. Grubbs, C. Linardich, J. A. Moore, I. C. Romero, D. Schlenk, and K. Strongin. 2022. A comprehensive petrochemical vulnerability index for marine fishes in the Gulf of Mexico. Science of the Total Environment 820: 152892. Available at: Sci Total Environ.

New England Seamount References

Auster, P. J., Moore, J. A., Heinonen, K., and Watling, L. 2005. A habitat classification scheme for seamount landscapes: assessing the functional role of deepwater corals as fish habitat. In: Freiwald, A., Roberts, J. M., editors. Cold-water Corals and Ecosystems. Springer-Verlag; p 761–769.

Cárdenas, P., and Moore, J. A. 2019. First records of Geodia demosponges from the New England Seamounts, an opportunity to test the use of DNA mini-barcodes on museum specimens. Marine Biodiversity 49:163–174. Available at: Journal

Kiraly, S. J., Moore, J. A., and Jasinski, P. H. 2005. Non-federally managed Atlantic deepwater and other sharks. Marine Fisheries Review 65(4):1–63. Available at: NOAA

Moore, J. A. et al. 2005. Selected fauna of Bear Seamount (New England Seamount chain) and the presence of “natural invader” species. Archives of Fishery and Marine Research 51(1–3):217–226. Available at: ResearchGate

Moore, J. A., Hartel, K. E., Craddock, J. E., and Galbraith, J. K. 2003. An annotated list of deepwater fishes from off New England, with new area records. Northeastern Naturalist 10(2):159–248. Available at: JSTOR

Moore, J. A. et al. 2003. Biodiversity of Bear Seamount, New England seamount chain: results of exploratory trawling. Journal of Northwest Atlantic Fisheries Science 31:363–372. Available at: Journal

Moore, J. A., Auster, P. J. 2009. Commensalism between juvenile cusk eels and pancake urchins on western North Atlantic Seamounts. Bulletin of the Peabody Museum of Natural History (Yale University) 50(2):381–386. Available at: Journal

Quattrini, A. M., Nizinski, M., Chaytor, J., Demopoulos, A., Roark, E. B., France, S., Moore, J. A., Heyl, T., Auster, P., Kinlan, B., Ruppel, C., Elliott, K., Kennedy, B., Lobecker, E., Sharke, A., and Shank, T. 2015. Exploration of submarine canyons off the northeastern United States reveals dynamic habitats and diverse ecosystems. PLoS One 10(10):e0139904. Available at: Journal

Stabile, F. A., Watkins-Colwell, G. J., Moore, J. A., Vecchione, M., and Burtt, E. H. 2017. Observations of wayward passerines and a falcon from a research vessel in the Western North Atlantic Ocean. Wilson Journal of Ornithology 129(2):349–353. Available at: Journal

Fish Phylogeny and Nomenclature

Phylogenetic Studies of Fishes

Dornburg, A., J. P. Townsend, W. Brooks, E. Spriggs, R. I. Eytan, J. A. Moore, P. C. Wainwright, A. Lemmon, E. Lemmon, and T. J. Near. 2017. New Insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset. Molecular Phylogenetics and Evolution 110: 27–38. Available at: MPE.

Dornburg, A., J. A. Moore, R. Webster, et al. Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei: Beryciformes: Holocentridae): Reconciling more than 100 Years of taxonomic confusion. Mol Phyl Evo 65, no. 2 (2012): 727–38. Available at: MPE.

Moore, J. A. 1993. The Phylogeny of the Trachichthyiformes (Teleostei: Percomorpha). Bulletin of Marine Science 52, no. 1: 114–36.

Near, T. J., A. Dornburg, R. I. Eytan, B. C. Keck, W. L. Smith, K. L. Kuhn, J. A. Moore, et al. 2013. Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes. Proceedings of the National Academy of Sciences 110, no. 31 (2013): 12738–43. Available at: PNAS.

Near, T. J., R. I. Eytan, A. Dornburg, K. L. Kuhn, J. A. Moore, et al. 2012. Resolution of ray-finned fish phylogeny and Timing of Diversification. Proceedings of the National Academy of Sciences 109, no. 34: 13698–703. Available at: PNAS.

Song, H. Y., K. Mabuchi, T. P. Satoh, J. A. Moore, et al. 2014. Mitogenomic circumscription of a novel percomorph fish clade mainly comprising ‘Syngnathoidei’ (Teleostei). Gene 542, no. 2: 146–55. Available at: Gene.

Stiassny, M. L. J., and J. A. Moore. 1992. A Review of the Pelvic Girdle of Acanthomorph Fishes, with Comments on Hypotheses of Acanthomorph Intrarelationships. Zoological Journal of the Linnean Society (London) 104, no. 3 (1992): 209–42. Available at: Zool J Linn Soc

Contributions to the Phylonyms Volume

Moore, Jon A., and Near Thomas A. 2020a. Actinopterygii. In: Phylonyms: Phylocode Companion Volume. CRC Press: p. 695–699.

Moore, Jon A., and Near Thomas A. 2020b. Pan-Actinopteri. In: Phylonyms: Phylocode Companion Volume. CRC Press: p. 701–703.

Moore, Jon A., and Near Thomas A. 2020c. Pan-Neopterygii. In: Phylonyms: Phylocode Companion Volume. CRC Press: p. 709–710.

Moore, Jon A., and Near Thomas A. 2020d. Actinopteri. In: Phylonyms: Phylocode Companion Volume. CRC Press: p. 705–708.

Moore, Jon A., and Near Thomas A. 2020e. Neopterygii. In: Phylonyms: Phylocode Companion Volume. CRC Press: p. 711–714.

Moore, Jon A., and Near Thomas A. 2020f. Osteichthyes. In: Phylonyms: Phylocode Companion Volume. CRC Press: p. 685–689.

Moore, Jon A., and Near Thomas A. 2020g. Pan-Actinopterygii. In: Phylonyms: Phylocode Companion Volume. CRC Press: p. 691–693.

Moore, Jon A., and Near Thomas A. 2020h. Pan-Osteichthyes. In: Phylonyms: Phylonyms: Phylocode Companion Volume. CRC Press: p. 681–683.

Moore, Jon A., and Near Thomas A. 2020i. Teleostei. In: Phylonyms: Phylocode Companion Volume. CRC Press: p. 719–723.

Moore, Jon A., and Near Thomas A. 2020j. Pan-Teleostei. In: Phylonyms: Phylocode Companion Volume. CRC Press: p. 715–717.

Gopher Tortoise Publications

Hanish, C. J., S. Velez, J. A. Moore, and C. D. Anderson. 2020. Endozoochory of Chrysobalanus icaco (Cocoplum) by the Gopherus polyphemus (Gopher tortoise) facilitates rapid germination and colonization in a suburban nature preserve. AoB PLANTS 12, no. 4: plaa024. Available at: AoB PLANTS

Moore, J. A., and A. Dornburg. 2024. Ingestion of fossil seashells, stones, and small mammal bones by gravid gopher tortoises (Gopherus polyphemus) in south Florida. Bulletin of the Peabody Museum of Natural History 55, no. 1 (2014): 55–63. Available at: Bull Peabody Mus Nat Hist

Moore, Jon A., M. Strattan, and V. Szabo. 2009. Evidence for year-round reproduction in a population of the gopher tortoise from southern Florida. Bulletin of the Peabody Museum of Natural History 50, no. 2: 387–92. Available at: Research Gate

Moore, Jon A., R. M. Engeman, H. T. Smith, and J. Woolard. 2006. Gopherus polyphemus (Gopher tortoise). Coyote predation. Herpetological Review 37, no. 1: 78–79.

Page-Karjian, A., K. Rafferty, C. Xavier, N. I. Stacy, J. A. Moore, S. E. Hirsch, S. Clark, C. A. Manire, and J. R. Perrault. 2021. Comprehensive health assessment and blood analyte reference intervals of gopher tortoises (Gopherus polyphemus) in southeastern Florida, USA. Conservation Physiology 9, no. 1: coab015. Available at: Conserv Physiol

Wetterer, J. K., R. C. Jones, J. Moore, J. and V. Viluan, V. 2025. Stinging ant species at gopher tortoise burrows change over time with habitat change. Sociobiology 72(4): e11787. Available at: Sociobiol

Wetterer, James K., and J. A. Moore. 2005. Red imported fire ants (Hymenoptera: Formicidae) at gopher tortoise (Testudines: Testudinidae) burrows. Florida Entomologist 88, no. 4: 349–54. Available at: Fla Entomol

Whitfield, S. M., J. P. Scholl, E. Frazier, K. Hendrickson, A. Figueroa, L. Gapczynski, R. Schneider, O. Rothberg, J. Genassia, and J. Moore. 2024. Status, distribution, and management of gopher tortoise in highly urbanized southeast Florida. Southeastern Naturalist 23, no. 3: 385–400. Available at: Southeast Nat