Publications

The PDF downloads on this page are provided "for purposes such as criticism, comment, news reporting, teaching (including multiple copies for classroom use), scholarship, or research." If you agree to use this material solely under the provisions for “fair use,” click on the year link to download a copy of the listed publication. The open access publications are available to use as allowed by their individual licenses.

Book

Wheeler, W.C., Aagesen, L., Arango, C.P., Faivovich, J., Grant, T., D'Haese, C., Janies, D., Smith, W.L., Varón, A., and Giribet, G. 2006. Dynamic Homology and Phylogenetic Systematics: A Unified Approach Using POY. American Museum of Natural History, New York. ISBN 0-913424-58.7.

Peer-reviewed Articles

2020s

Ghedotti, M.J., Gonzalez, F.M.,Riggin, K., Agudo, K.C., Davis, M.P., Smith, W.L., and Frable, B.W.. In Press. Anatomy and evolution of bioluminescent organs in the gulper eels (Anguilliformes: Saccopharyngoidea). *Ichthyology & Herpetology*

DeArmon, E.S., Smith, W.L., and Davis, M.P. 2026. Dragons of the deep (Stomiiformes: Stomiidae): Evolutionary relationships and taxonomy of the barbeled dragonfishes (Stomiinae) and viperfishes (Chauliodontinae). Zootaxa 5759:1–25.

May, Z.A., Smith, W.L., and Davis, M.P. 2026. The evolutionary relationships of marine hatchetfishes (Stomiiformes: Sternoptychidae) based on genomic and morphological data. Zootaxa 5757:449–466.

Maile, A.J., Smith, W.L., and Davis, M.P. 2025. A total-evidence phylogenetic approach to understanding the evolution, depth transitions, and body-shape changes in the anglerfishes and allies (Acanthuriformes: Lophioidei). PLoS ONE 20:e0322369.

Martin, R.P. and Smith, W.L. 2024 First evidence of sexual dimorphism in olfactory organs of deep-sea lanternfishes (Myctophidae). Peerj 12:e17075.

Smith, W.L., Girard, M.G., Walker, Jr., H.J., and Davis, M.P. 2024 The phylogeny of bristlemouths, lightfishes, and portholefishes with a revised family-level classification of the dragonfishes (Teleostei: Stomiiformes). NOAA Professional Paper NMFS 24:167–184.

Turner, T.F., Bart, Jr., H.L., McCormick, F., Besser, A.C., Bowes, R.E., Capps, K.A., DeArmon, E.S., Dillman, C.B., Driscoll, K.P., Dugger, A., Hamilton, G.L., Harris, P.M., Hendrickson, D.A., Hoffman, J., Knouft, J.H., Lepak, R.F., López-Fernández, H., Montaña, C.G., Newsome, S.D., Pease, A.A., Smith, W.L., Taylor, C.A., and Welicky, R.L. 2023. Long-term ecological research in freshwaters enabled by regional biodiversity collections, stable isotope analysis, and environmental informatics. BioScience 73:479–493.

Smith, W.L., Ghedotti, M.J., Domínguez-Domínguez, O., McMahan, C.D., Espinoza, E., Martin, R.P., Girard, M.G., and Davis, M.P. 2022. Investigations into the ancestry of the Grape-eye Seabass (Hemilutjanus macrophthalmos) reveal novel limits and relationships for the Acropomatiformes (Teleostei: Percomorpha). Neotropical Ichthyology 20:e210160.

Sparks, J.S. and Smith, W.L. 2022. Pantanodontidae: Pantanodon. Pages 1271–1272. In: The New Natural History of Madagascar. Goodman, S. (ed.). Princeton University Press, Princeton, New Jersey.

Smith, W.L. 2022. Classification of serranoid fishes. Page 32. In: Coastal Fishes of the Western Indian Ocean, Volume 3. Heemstra, P. and Heemstra, E. (eds.). South African Institute for Aquatic Biology, Grahamstown, South Africa.

Martin, R.P., Davis, M.P., and Smith, W.L. 2022. The impact of evolutionary trade-offs among bioluminescent organs and body shape in the deep sea: a case study on lanternfishes. Deep Sea Research Part I: Oceanographic Research Papers 184:103769.

Girard, M.G., Davis, M.P., Baldwin, C.C., Dettaï, Martin, R.P., and Smith, W.L. 2022. Molecular phylogeny of the threadfin fishes (Polynemidae) using ultraconserved elements. Journal of Fish Biology 100:793–810.

Girard, M.G., Davis, M.P., Tan, H., Wedd, D.J., Chakrabarty, P., Ludt, W.B., Summers, A.P., and Smith, W.L. 2022. Phylogenetics of archerfishes (Toxotidae) and evolution of the toxotid shooting apparatus. Integrative Organismal Biology 4:obac013. (cover article)

Ghedotti, M.J. DeKay, H.M., Maile, A.J., Smith, W.L., and Davis, M.P. 2021. Anatomy and evolution of bioluminescent organs in the slimeheads (Teleostei: Trachichthyidae). Journal of Morphology 282:820–832.

Girard, M.G., Davis, M.P., and Smith, W.L. 2020. The phylogeny of carangiform fishes: morphological and genomic investigations of a new fish clade. Copeia 108: 265–298.

2010s

Ghedotti, M.J., Smith, W.L., and Davis M.P. 2019. The first evidence of intrinsic epidermal bioluminescence within ray-finned fishes in the snaketooth fish Pseudoscopelus scriptus (Chiasmodontidae). Journal of Fish Biology 95:1540–1543.

Ghedotti, M.J., Gruber, J.N., Barton, R.W., Davis, M.P., and Smith, W.L. 2018. Morphology and evolution of bioluminescent organs in the glowbellies (Percomorpha: Acropomatidae) with comments on the taxonomy and phylogeny of Acropomatiformes. Journal of Morphology 279:1640–1653.

Smith, W.L., Buck, C.A., Ornay, G.S., Davis, M.P., Martin, R.P., Gibson, S.Z., and Girard, M.G. 2018. Improving vertebrate skeleton images: Fluorescence and the non-permanent mounting of cleared-and-stained specimens. Copeia 106:427–435.

Smith, W.L., Everman, E., and Richardson, C. 2018. Phylogeny and taxonomy of flatheads, scorpionfishes, sea robins, and stonefishes (Percomorpha: Scorpaeniformes) and the evolution of the lachrymal saber. Copeia 106:94–119.

Martin, R.P., Olson, E.E., Girard, M.G., Smith, W.L., and Davis, M.P. 2018. Light in the darkness: New perspective on lanternfish relationships and classification using genomic and morphological data. Molecular Phylogenetics and Evolution 121:71–85.

Harrington, R.C., Faircloth, B.C., Eytan, R.I., Smith, W.L., Near, T.J., Alfaro, M.E., and Friedman, M. 2016. Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye. BMC Evolutionary Biology 16:224.

Girard, M.G. and Smith, W.L. 2016. The phylogeny of marine sculpins of the genus Icelinus with comments on the evolution and biogeography of the Pseudoblenninae. Zootaxa 4171:549–561.

Smith, W.L. 2016. Uranoscopidae. Pages 2786–2792. In: The Living Marine Resources of the Eastern Central Atlantic. Carpenter, K. (ed.). FAO Species Identification Guide for Fishery Purposes. FAO, Rome.

Smith, W.L. 2016. Trachinidae. Pages 2769–2779. In: The Living Marine Resources of the Eastern Central Atlantic. Carpenter, K. (ed.). FAO Species Identification Guide for Fishery Purposes. FAO, Rome.

Smith, W.L. 2016. Pinguipedidae. Pages 2767–2768. In: The Living Marine Resources of the Eastern Central Atlantic. Carpenter, K. (ed.). FAO Species Identification Guide for Fishery Purposes. FAO, Rome.

Smith, W.L. 2016. Chiasmodontidae. Pages 2764–2766. In: The Living Marine Resources of the Eastern Central Atlantic. Carpenter, K. (ed.). FAO Species Identification Guide for Fishery Purposes. FAO, Rome.

Smith, W.L., Stern, J.H., Girard, M.G., and Davis, M.P. 2016. Evolution of venomous cartilaginous and ray-finned fishes. Integrative and Comparative Biology 56:950–961.

Davis, M.P., Sparks, J.S., and Smith, W.L. 2016. Repeated and widespread evolution of bioluminescence in marine fishes. PLoS ONE 11:e0155154.

Gruber, D.F., Loew, E.R., Deheyn, D.D., Akkaynak, D., Gaffney, J.P., Smith, W.L., Davis, M.P., Stern, J.H., Pieribone, V.A., and Sparks, J.S. 2016. Biofluorescence in catsharks (Scyliorhinidae): Fundamental description and relevance for elasmobranch visual ecology. Nature: Scientific Reports 6:24751.

Smith, W.L. and Busby, M.S. 2014. Phylogeny and taxonomy of sculpins, sandfishes, and snailfishes (Perciformes: Cottoidei) with comments on the phylogenetic significance of their early-life-history specializations. Molecular Phylogenetics and Evolution 79:332–352.

Price, S.A., Schmitz, L., Oufiero, C.E., Eytan, R.I., Dornburg, A., Smith, W.L., Friedman, M., Near, T.J., and Wainwright, P.C. 2014. Two waves of colonization straddling the K–Pg boundary formed the modern reef fish fauna. Proceedings of the Royal Society of London, B 281:20140321.

Stewart, T.A., Smith, W.L., and Coates, M.I. 2014. The origins of adipose fins: An analysis of homoplasy and the serial homology of vertebrate appendages. Proceedings of the Royal Society of London, B 281:20133120.

Davis, M.P., Holcroft, N.I., Wiley, E.O., Sparks, J.S., and Smith, W.L. 2014. Species-specific bioluminescence facilitates speciation in the deep sea. Marine Biology 161:1139–1148.

Sparks, J.S., Schelly, R.C., Smith, W.L., Davis, M.P., Tchernov, D., Pieribone, V.A., and Gruber, D.F. 2014. The covert world of fish biofluoresence: A phylogenetically widespread and phenotypically variable phenomenon. PLoS ONE 9:e83259.

McMahan, C.D., Chakrabarty, P., Sparks, J.S., Smith, W.L., and Davis, M.P. 2013. Temporal patterns of diversification across global cichlid biodiversity (Acanthomorpha: Cichlidae). PLoS ONE 8:e71162.

Near, T.J., Dornburg, A., Eytan, R.I., Keck, B.P., Smith, W.L., Kuhn, K.L., Moore, J.A., Price, S.A., Burbrink, F.T., Friedman, M., and Wainwright, P.C. 2013. Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes. Proceedings of the National Academy of Sciences 110:12738–12743.

Borden, W.C., Grande, T., and Smith, W.L. 2013. Comparative osteology and myology of the caudal fin in the Paracanthopterygii (Teleostei: Acanthomorpha). Pages 419–455. In: Mesozoic Fishes 5–Global Diversity and Evolution. Arratia, G., Schultze, H.-P., and Wilson, M.V.H. (eds.). Verlag Dr. Friedrich Pfeil, München, Germany.

Grande, T., Borden, W.C., and Smith, W.L. 2013. Limits and relationships of Paracanthopterygii: A molecular framework for evaluating past morphological hypotheses. Pages 385–418. In: Mesozoic Fishes 5–Global Diversity and Evolution. Arratia, G., Schultze, H.-P., and Wilson, M.V.H. (eds.). Verlag Dr. Friedrich Pfeil, München, Germany.

Dikow, R.B. and Smith, W.L. 2013. Complete genome sequences provide a case study for the evaluation of gene-tree thinking. Cladistics 29:672–682.

Dikow, R.B. and Smith, W.L. 2013. Genome-level homology and phylogeny of Vibrio + Photobacterium (Grammaproteobacteria: Vibrionales: Vibrionacaea) with new complete genome sequences. BMC Microbiology 13:80.

Miller, J., Dikow, T., Agosti, D., Sautter, G., Catapano, T., Penev, L., Zhang, Z.Q., Pentcheff, D., Pyle, R., Blum, S.D., Parr, C., Freeland, C., Garnett, T., Ford, L.S., Muller, B., Smith, W.L., Strader, G., Georgiev, T., and Bénichou, L. 2012. From taxonomic literature to cybertaxonomic content. BMC Biology 10:87.

Wainwright, P.C., Smith, W.L., Price, S.A., Tang, K.L., Sparks, J.S., Ferry, L.A., Kuhn, K.L., Eytan, R.I., and Near, T.J. 2012. The evolution of pharyngognathy: A phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond. Systematic Biology 61:1001–1027.

Near, T.J., Eytan, R.I., Dornburg, A., Kuhn, K.L., Moore, J.A., Davis, M.P., Wainwright, P.C., Friedman, M., and Smith, W.L. 2012. Resolution of ray-finned fish phylogeny and timing of diversification. Proceedings of the National Academy of Sciences 109:13698–13703.

Near, T.J., Sandel, M., Kuhn, K.L., Unmack, P.J., Wainwright, P.C., and Smith, W.L. 2012. Nuclear gene-inferred phylogenies resolve the relationships of the enigmatic Pygmy Sunfishes, Elassoma (Teleostei: Percomorpha). Molecular Phylogenetics and Evolution 63:388–395.

Wiley, E.O., Chakrabarty, P., Craig, M.T., Davis, M.P., Holcroft, N.I., Mayden, R.L., and Smith, W.L. 2011. A response to Mooi, Williams and Gill. Zootaxa 2946:33–37.

Wiley, E.O., Chakrabarty, P., Craig, M.T., Davis, M.P., Holcroft, N.I., Mayden, R.L., and Smith, W.L. 2011. Will the real phylogeneticists please stand up? Zootaxa 2946:7–16.

Li, C., Betancur-R, R., Smith, W.L., and Ortí, G. 2011. Monophyly and interrelationships of Snook and Barramundi (Centropomidae sensu Greenwood) and five new markers for fish phylogenetics. Molecular Phylogenetics and Evolution 60:463–471.

Chakrabarty, P., Davis, M.P., Smith, W.L., Baldwin, Z.H., and Sparks, J.S. 2011. Is sexual selection driving diversification of the bioluminescent ponyfishes (Teleostei: Leiognathidae)? Molecular Ecology 20:2818–2834.

Chakrabarty, P., Davis, M.P., Smith, W.L., Berquist, R., Gledhill, K., Frank, L., and Sparks, J.S. 2011. Evolution of the light organ system in ponyfishes (Teleostei: Leiognathidae). Journal of Morphology 272:704–721.

Smith, W.L. 2010. Promoting resolution of the percomorph bush: A reply to Mooi and Gill. Copeia 2010:520–524.

Jones, C.C., Smith, W.L., and Sparks, J.S. 2010. A new species of rainbowfish (Teleostei: Melanotaenioidei: Bedotiidae) from the Makira region of northeastern Madagascar. Copeia 2010:284–291.

2000s

Smith, W.L., Smith, K.R., and Wheeler, W.C. [2009]. Novel mitochondrial intergenic spacer in fairy basslets (Serranidae: Anthiinae) and the simultaneous analysis of nucleotide and genomic data. American Museum Novitates 3652:1–10.

Smith, W.L., Chakrabarty, P., and Sparks, J.S. 2008. Phylogeny, taxonomy, and evolution of Neotropical cichlids (Teleostei: Cichlidae: Cichlinae). Cladistics 24:625–641.

Smith, W.L. and Sparks, J.S. 2007. Case 3383: Gobius lagocephalus Pallas 1770 (currently Sicyopterus lagocephalus: Teleostei, Gobiidae): Proposed suppression of the specific name. Bulletin of the International Code of Zoological Nomenclature 64:103–107.

Smith, W.L. and Sparks, J.S. 2007. Gobius lagocephalus: The world's most widespread nomen dubium. Molecular Phylogenetics and Evolution 43:696–698.

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

Webb, J.F., Smith, W.L., and Ketten, D.R. 2006. The laterophysic connection and swim bladder of butterflyfishes in the genus Chaetodon (Perciformes: Chaetodontidae). Journal of Morphology 267:1338–1355.

Sparks, J.S. and Smith, W.L. 2006. Sicyopterus lagocephalus: Widespread species, species complex, or neither? A critique on the use of molecular data for species identification. Molecular Phylogenetics and Evolution 40:900–902.

Smith, W.L. and Wheeler, W.C. 2006. Venom evolution widespread in fishes: A road map for the bioprospecting of piscine venoms. Journal of Heredity 97:206–217.

Sparks, J.S., Dunlap, P.V., and Smith, W.L. 2005. Evolution and diversification of a sexually dimorphic luminescent system in ponyfishes (Teleostei: Leiognathidae), including diagnoses for two new genera. Cladistics 21:305–327. (Cover Article)

Sparks, J.S. and Smith, W.L. 2005. Freshwater fishes, dispersal ability, and non-evidence: "Gondwana life rafts" to the rescue. Systematic Biology 54:158–165.

Sparks, J.S. and Smith, W.L. 2004. Phylogeny and biogeography of cichlid fishes (Teleostei: Perciformes: Cichlidae). Cladistics 20:501–517. (Cover Article)

Greenfield, D.W. and Smith, W.L. 2004. Allenbatrachus meridionalis, a new toadfish (Batrachoididae) from Madagascar and Reunion. Proceedings of the California Academy of Sciences 55:570–574.

Sparks, J.S. and Smith, W.L. 2004. Phylogeny and biogeography of the Malagasy and Australasian rainbowfishes (Teleostei: Melanotaenioidei): Gondwanan vicariance and evolution in freshwater. Molecular Phylogenetics and Evolution 33:719–734.

Smith, W.L. and Wheeler, W.C. 2004. Polyphyly of the mail-cheeked fishes (Teleostei: Scorpaeniformes): Evidence from mitochondrial and nuclear sequence data. Molecular Phylogenetics and Evolution 32:627–646.

Rosenblatt, R.H. and Smith, W.L. 2004. Icelinus limbaughi, a new species of sculpin (Teleostei: Cottidae) from southern California. Copeia 2004:556–-561.

Smith, W.L., Webb, J.F., and Blum, S.D. 2003. The evolution and phylogenetic significance of the laterophysic connection with a revised phylogeny and classification of butterflyfishes (Teleostei: Chaetodontidae). Cladistics 19:287–306. (Cover Article)

Smith, W.L. 2003. Scorpaeniformes I: Gurnards and flatheads. Pages 157–162. In: Grzimek's Animal Life Encyclopedia: Fishes Volume 2. Thoney, D., Loiselle, P., and Schlager, N. (eds.). The Gale Group, Farmington Hills, MI.

Smith, W.L. 2003. Scorpaeniformes II: Scorpionfishes and relatives. Pages 163–178. In: Grzimek's Animal Life Encyclopedia: Fishes Volume 2. Thoney, D., Loiselle, P., and Schlager, N. (eds.). The Gale Group, Farmington Hills, MI.

Webb, J.F. and Smith, W.L. 2000. The laterophysic connection in chaetodontid butterfly-fishes: Morphological variation and speculations on sensory function. Philosophical Transactions of the Royal Society of London, B 355:1125–1129.

1990s

Baldwin, C.C. and Smith, W.L. 1998. Belonoperca pylei, a new species of seabass (Teleostei: Serranidae: Epinephelinae: Diploprionini) from the Cook Islands with comments on relationships among diploprionins. Ichthyological Research 45:325–339.

Editorial Article

Smith, W.L. 2021. Introduction to Ichthyology & Herpetology. Ichthyology & Herpetology 109:1–2.