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.
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. accepted pending revision. 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 for Vibrio costicola, Photobacterium gazogenes, and Photobacterium logei. 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.
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 butteryflyfishes in the genus Chaetodon (Perciformes: Chaetodontidae). Journal of Morphology 267:1338-1355.
Wheeler, W.C., Aagesen, L., Arango, C.P., Faivovich, J., Grant, T., D’Haese, C., Janies, D., Smith, W.L., Varon, 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.
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.
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.
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.
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, Series B 355:1125-1129.
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.