159. Peloso, P.L.V., D.R. Frost, C.J. Raxworthy, W.C. Wheeler. 2017. Nomenclatural stability does not justify recognition of paraphyletic taxa: a response to Scherz et al. (2016). Molecular Phylogenetics and Evolution, in press.

158. Wheeler, W. C., J. A. Coddington, L. M. Crowley, D. Dimitrov, P. A. Goloboff, C. E. Griswold, G. Hormiga, L. Prendini, M. J. Ramírez, P. Sierwald, L. Almeida-Silva, F. Alvarez-Padilla, M. A. Arnedo, L. R. Benavides-Silva, S. P. Benjamin, J. E. Bond, C. J. Grismado, E. Hasan, M. Hedin, M. A. Izquierdo, F. M. Labarque, J. Ledford, L. Lopardo, W. P. Maddison, J. A. Miller, L. N. Piacentini, N. I. Platnick, D. Polotow, D. Silva-Dávila, N. Scharff, T. Szuts, D. Ubick, C. J. Vink, H. M. Wood, and J. Zhang. The spider tree of life: Phylogeny of Araneae based on target-gene analyses from an extensive taxon sampling. 2017. Cladistics, in press.

156. Clouse, B. Blanchard, R. Gibson, W. C. Wheeler, and R. M. Janda. 2016. Taxonomic updates for some confusing Micronesian Camponotus (Hymenoptera: Formidicidae: Formicinae). Myrmecological News, 23:139-152.

155. Wheeler, W. C. 2016. Computational aspects of the phylogenetic analysis of comparative sequence data. In Igor Pavlov eds. Aspects of Biodiversity. Archives of Zoological Museum of Lomonosov Moscow State University. 38:99-115.

154. Sharma, P. S. , R. M. Clouse, and W. C. Wheeler. 2016. Hennig’s semaphoront concept and the use of ontogenetic stages in phylogenetic reconstruction. Cladistics 25:1-16.

153. Ford, E., and W. C. Wheeler. 2016. Comparison of Heuristic Approaches to the General-Tree-Alignment Problem. Cladistics, 32:452-460.

152. Wheeler, W. C., and G. Giribet. 2016. “Molecular data in systematics: a promise fulfilled, a future beckoning.” pp 329.344. in The Future of Phylogenetic Systematics: The Legacy of Willi Hennig. Q. Wheeler, D. Williams, and M. Schmitt Eds.

151. Clouse, R. M. , P. R. Sharma, J. C. Stuart, L. R. Davi, G. Giribet, S. L. Boyer, W. C. Wheeler. 2015. Phylogeography of the harvestman Metasiro (Arthropoda, Arachnida, Opiliones) reveals a potential solution to the Pangean paradox. Organisms, Diversity, and Evolution, 1-18.

150. Sharma, P. P., M. A. Santiago, E. González-Santillán, L. Monod, and W. C. Wheeler. 2015. Evidence of duplicated Hox genes in the most recent common ancestor of extant scorpions. Evolution and Development 17:347-355..

149. Wheeler, W. C. Phylogenetic Network Analysis as a Parsimony Optimization Problem. 2015. BMC Bioinformatics. 16:296.

148. Sharma, P. P., O. A. Tarazona, D. H. Lopez, E. E. Schwager, M. J. Cohn, W. C. Wheeler, C. G. Extavour. 2015. A conserved genetic mechanism specifies deutocerebral appendage identity in insects and arachnids. Proceedings of the Royal Society B, 282:20150698.

147. Grace-Lema, Danielle; Yared, Solomon; Quitadamo, Andrew; Janies, Daniel; Wheeler, Ward; Balkew, Meshesha; Hailu, Asrat; Warburg, Alon; Clouse, Ronald. 2015. “A molecular phylogeny of sand flies (Diptera : Psychodidae : Phlebotominae), using recent Ethiopian collections and a broad selection of public sequence data.” Systematic Entomology, 40 (4), 733-744.

146. Peloso, P. L. V. D. R. Frost, S. J. Richards, M. Rodrigues, S. Donnellan, M. Matsui, C. J. Raxworthy, S. D. Biju, E. M. Lemmon, A. R. Lemmon, and W. C. Wheeler. 2015. The Impact of Anchored Phylogenomics and Taxon Sampling on Phylogenetic Inference in Narrowmouthed Frogs (Anura, Microhylidae). Cladistics, 19 MAR 2015, DOI: 10.1111/cla.12118.

145. McMahan, C. D. , L. R. Freeborn, W. C. Wheeler, and B. I. Crother. Forked tongues revisited: molecular apomorphies support morphological hypotheses of squamate evolution. 2015. Copeia, 103 (3), 525-529.

144. Clouse, R. M. Janda, B. Blanchard, P. Sharma, B. Hoffman, A. Andersen, J. Czekanski-Moir, P. Krushelnycky, C. Rabeling, E. Economo, E. Sarnat, D. General, G. Alpert, W. C. Wheeler. Molecular phylogeny of an Indo-Pacific carpenter ant (Hymenoptera : Formicidae, Camponotus) reveals waves of dispersal and colonization from diverse sources. Cladistics 31:424-437.

143. Wheeler, W. C., N. Lucaroni, L. Hong, L. M. Crowley, and A. Varón. 2015. POY version 5: Phylogenetic analysis using dynamic homologies under multiple optimality criteria. Cladistics 31:189-196.

142. Wheeler, W. C. and P. M. Whiteley. 2015. Historical Linguistics as a Sequence Optimization Problem: Uto-Aztecan Language Evolution and Biogeography. Cladistics 31:113-125

141. Pedraza, P., N. R. Salinas, A.  L. Virnig, and W. C. Wheeler. 2015. Preliminary phylogenetic analysis of the Andean clade and the placement of new Colombian blueberries (Ericaceae, Vaccinieae). PhytoKeys 49: 13-31.

140. Ford, E. K. St. John, and W. C. Wheeler. 2015. Towards Improving Searches for Optimal Phylogenies. Sys. Biol. 64:56-65.

139. Sharma, P., and W. C. Wheeler. 2014. Cross-bracing uncalibrated nodes in molecular dating improves congruence of fossil and molecular age estimates. Frontiers in Zoology, 11:57.

138. Sharma, P. P., S. Kaluziak, A. R. Perez-Porro, V. L. González, G. Hormiga, W. C. Wheeler, and G. Giribet. 2014. Phylogenomic interrogation of Chelicerata reveals systemic conflicts in phylogenetic signal. Mol. Biol. Evol. 31:2963-2984.

137. Sharma, P. P., E. E. Schwager, C. G. Extavour, and W. C. Wheeler. 2014. Hox gene duplications correlate with posterior heteronomy in scorpions. Proc. Royal Soc. B., 281:20140661.

136. Clouse, R. M. and W. C. Wheeler. 2014. Descriptions of two new, cryptic species of Metasiro (Arachnida: Opiliones: Cyphophthalmi: Neogoveidae) from South Carolina, USA, including a discussion of mitochondrial mutation rates. Zootaxa, 3814: 177–201.

135. Sharma, P. P., T. Gupta, E. E. Schwager, W. C. Wheeler, C. G. Extavour. 2014. Subdivision of cap-n-collar expression domains constitutes a mandibulate synapomorphy. J. Evo Devo., 5:1-11.

134. Peloso, P. L., M. J. Sturaro, M. C. Forlani, P. Gaucher, A. P. Motta, and W. C. Wheeler. 2014. Phylogeny, taxonomic revision, and character evolution of the genera Chiasmocleis and Syncope (Anura: Microhylidae) in the Amazonia, with descriptions of three new species. Am. Mus. Novitates, 386:1-113.

133. Wheeler, W. C. Phyletic Groups on Networks. 2014. Cladistics 30:447-451

132. Kannan, L., and W. C. Wheeler. 2014. On exactly computing the parsimony scores on phylogenetic networks using dynamic programming. Journal of Computational Biology, 21:303-319.

131. Faivovich, J. Padial, S. Castroviejo-Fisher, M. M. Lyra, B. V. M. Berneck, P. P. Iglesia, P. J. R. Kok, R. D. MacCulloch, M. T. Rodrigues, V. K. Verrdade, C. P. Torres Gastello, J. C. Chaparro, P. H. Valdujo, S. Reichle, J. Moravec, V. Gvoždík, G. Gagliardi-Urrutia, R. Ernst, I. De La Riva, D. B. Means, A. P. Lima, J. Celsa Señaris, W. C. Wheeler, and C. F. B. Haddad. 2013. Systematics of spiny-backed treefrogs (Hylidae: Ostecephalus): an Amazonian puzzle. Zool. Scripta 42:351-380.

130. Wheeler, W. C. 2014. Maximum a Posteriori Probability Assignment (MAP-A): An Optimality Criterion for Phylogenetic Trees via Weighting and Dynamic Programming. Cladistics 30:282-290.

129. Payne A, Barden P, Wheeler W. C., Carpenter J. M. 2013 Direct optimization and the evolution of the hymenopteran superfamilies. Am. Mus. Novitates 3789:1-19.

128. Sharma, P.P., J. D. Zardus, E. E. Boyle, V. L. González, R. M. Jennings, E. McIntyre, P. Bouchet, W. C. Wheeler, R. J. Etter G. Giribet. 2013. Into the deep: A phylogenetic approach to the bivalve subclass Protobranchia. Mol. Phylo. and Evol., 69:188-204.

127. Sharma, P. and W. C. Wheeler. 2013. Revenant clades in historical biogeography: the geology of New Zealand predisposes endemic clades to root age shifts. J. Biogeography, 40:1609-1618.

126. Pedraza-Peñalosa, P., N. R. Salinas, and W. C. Wheeler. 2013. Venation patterns of neotropical blueberries (Vaccinieae: Ericaceae) and their phylogenetic utility. Phytotaxa, 96:1-53.

125. Varón, A, and W. C. Wheeler. 2013. Heuristics for the General Tree Alignment problem. BMC Bioinformatics, 14:66.

124. Clouse, R., Sharma, P., Giribet, G., and W. C. Wheeler. 2013. Elongation factor-1α, a putative single-copy nuclear gene, has divergent sets of paralogs in an arachnid. Molecular Phylogenetics and Evolution 68:471-481.

123. Blotto, B. L., J. J. Nuñez, N. G. Basso, C. A. Úbeda, W. C. Wheeler, J. Faivovich. 2013. Phylogenetic relationships of a Patagonian frog radiation, the Alsodes + Eupsophus clade (Anura: Cycloramphidae). Cladistics, 29:113-131.

122. Varón, A, and W. C. Wheeler. 2012. The Tree Alignment problem. BMC Bioinformatics, 13:293.

121. Faivovich, J., D. P. Ferraro, N.. G. Basso, C. F. B. Haddad, M. Trefaut Rodrigues, W. C. Wheeler, and E. O. Lavilla. 2012. A phylogenetic analysis of Pleurodema (Anura: Leptodactylidae: Leiuperinae) based on mitochondrial and nuclear gene sequences, with comments on the evolution of anuran foam nests. Cladistics 28:460-482.

120. Janies, D, L. W. Pomeroy, J. M. Aaronson, S. Handelman, J. Hardman, K. Kawalec, T. Bitterman, and W. C. Wheeler. 2012. Analysis and visualization of H7 influenza using genomic, evolutionary and geographic information in a modular web service. Cladistics 28:483-488.

119. Kannan, L., and W. C. Wheeler. 2012. Maximum Parsimony on Phylogenetic Networks. Algorithms for Molecular Biology, 7:9-19.

118. Denton, J. and W. C. Wheeler. 2012. Trivial alignments in maximum likelihood analysis of nucleotide data. Cladistics 28:514-528.

117. Wheeler, W. C. 2012. Trivial Minimization of Extra-Steps under Dynamic Homology. Cladistics 28:188-189.

116. Wheeler, W. C., P. M. Whiteley, and T. Powers. 2012. “Phylogenetic Analysis of Socio-Cultural Data: Identifying Transformation Vectors for Kinship Systems,” pp. 109-134 in Crow-Omaha: New Light on a Classic Problem of Kinship Analysis. P. M. Whiteley and T. R. Trautmann eds. University of Arizona Press.

115. Sharkey, M. J., J. M. Carpenter, L. Vilhelmsen, J. Heraty, D. Hawks, A. P. G. Dowling, S. Schulmeister, D. Murray, A. R. Deans, F. Ronquist, L. Krogmann, and W. C. Wheeler. 2012. Phylogenetic Relationships Among Superfamilies of Hymenoptera. Cladistics 28:80-112.

114. Heraty, J., F. Ronquist, J. M. Carpenter, D. Hawks, S. Schulmeister, A. P. Dowling, D. Murray, J. Munro, W.C. Wheeler, and N. Schiff. 2011. Evolution of the Hymenopteran Megaradiation. Mol. Phyl. and Evol., 60:73-88.

113. Janies, D. A., T. Treseder, B. Alexandrov, F. Habib, J. J. Chen R. Ferreira, Ü. Catalyürek, A. Varón, W. C. Wheeler. 2011. The Supramap project: Linking pathogen genomes with geography to fight emergent infectious diseases. Cladistics 27:61-66.

112. Wheeler, W. C. 2010. Distinctions between optimal and expected support. Cladistics 26:657-663.

111. Varón, A., Vinh, L. S., and W. C. Wheeler.  2010. POY version 4: phylogenetic analysis using dynamic homologies. Cladistics 26:72-85.

110. Faivovich, J., C. Haddad, D. Baeta, K-H. Jungfer, G. Álvares, R. Brandão, C. Sheil, L. S. Barrientos, C. Barrio-Amorós, C. A. G. Cruz, and W. C. Wheeler. 2010. The phylogenetic relationships of the charismatic poster frogs, Phyllomedusinae (Anura, Hylidae). Cladistics 26:227-261.

109. Hejnöl, A., M. Obst, A. Stamatakis, M. Ott, G. W. Rouse, G. D. Edgecombe, P. Martinez, J. Baguñà, X. Bailly, U. Jondelius, M. Wiens., W. E.G. Müller., E. Seaver, W. C. Wheeler, M. Q. Martindale, G. Giribet, and C. W. Dunn. 2009. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc. Royal. Soc. B. 276:4261 – 4270.

108. Wheeler, W. C. and G. Giribet. 2009. “Phylogenetic hypotheses and the utility of multiple sequence alignment,” pp 95-104, in M. Rosenberg eds., Sequence Alignment: Methods, Models, Concepts, and Strategies. University of California Press: Berkeley, CA.

107. Schuh, R.T., C. Weirauch, and W.C. Wheeler. 2009. Phylogenetic analysis of family-group relationships in the Cimicomorpha (Hemiptera). Systematic Entomology 34:15-48.

106. 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 rearrangement data. Am . Mus. Novitates:3652. 10pp.

105.  Varón, A., and W. C. Wheeler.  2008. Application note: on extension gap in POY version 3.  Cladistics 24:1070.

104. Wheeler, W. C. and K. M. Pickett.  2008. Topology-Bayes versus Clade-Bayes in Phylogenetic Analysis. Mol. Biol. Evol. 25:447-453.

103. Dunn, C. W., A. Hejnol, D. Q. Matus, K. Pang, W. E. Browne, S. A. Smith, E. Seaver, G. W. Rouse, M. Obst, G. D. Edgecombe, M. V. Sørensen, S. H.D. Haddock, A. Schmidt-Rhaesa, A. Okusu, R. M. Kristensen, W. C. Wheeler, M. Q. Martindale, and G. Giribet. 2008. Broad phylogenomic sampling improves resolution of the Animal Tree of Life. Nature 452:745-749.

102. Murienne, J., R. Pellens, R. B. Budinoff, W. C. Wheeler, and P. Grandcolas. 2008. Phylogenetic analysis of the endemic New Caledonian cockroach Lauraesilpha. Testing competing hypotheses of diversification.” Cladistics 24:802-812.

101. Grazia, J, R. T. Schuh. And W. C. Wheeler. 2008. Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera). Cladistics 24:932-976.

100. Frost, D. R., T. Grant, J. Faivovich, R. H. Bain, A. Haas , C. F. B. Haddad, R. O. de Sa, A. Channing, M. Wilkinson, S. C. Donnellan, C. J. Raxworthy, J. A. Campbell, B. L. Blotto, P. Moler, R. C. Drewes, R. A. Nussbaum, J. D. Lynch, D. M. Green, and W. C. Wheeler. 2008. Is The Amphibian Tree of Life really fatally flawed? Cladistics 24:385-395.

99. Wheeler, W. C. 2007. Chromosomal Character Optimization. Mol. Phyl. Evol. 44:1130-1140.

98. de Carvalho, M. R., F. A. Bockmann, D. S. Amorim, C. R. F. Brandão, M. de Vivo, J. L. de Figueiredo, H. A. Britski, M. C. C. de Pinna, N. A. Menezes, F. P. L. Marques, N. Papavero, E. M. Cancello, J. V. Crisci, J. D. McEachran, R. C. Schelly, J. G. Lundberg, A. C. Gill, R. Britz, Q. D. Wheeler, M. L. J. Stiassny, L. R. Parenti, L. M. Page, W. C. Wheeler, J. Faivovich, R. P. Vari, L. Grande, C. J. Humphries, R. DeSalle, M. C. Ebach, and G. J. Nelson. 2007. Taxonomic Impediment or Impediment to Taxonomy? A Commentary on Systematics and the Cybertaxonomic-Automation Paradigm. Evolutionary Biology 34:140-143.

97. Vinh, Ly Sy., A. Varon, D. Janies, and W. C. Wheeler. 2007. Towards phylogenomic reconstruction. Proceedings of the 2007 International Conference on Bioinformatics and Computational Biology. Las Vegas Nevada, USA, pp. 98-104.

96. Giribet, G, and W. C. Wheeler. 2007. The case for sensitivity: a response to Grant and Kluge. Cladistics 23:294-296.

95. Janies, A. W. Hill, E. Waltari, R. Guralnick, F. Habib, W. C. Wheeler. 2007. Genomic analysis and geographic visualization of the spread of avian influenza. Syst. Biol. 56:31-39.

94. Pellens, P., C. D’Haese, X. Bellés, M-D. Piulachs, F. Legendre, W. C. Wheeler, P. Grandcolas. 2007. The evolutionary transition from subsocial to eusocial behavior in Dictyoptera: phylogenetic evidence for modification of the “shift-dependent-care” hypothesis with a new subsocial cockroach. Molecular Phylogenetics and Evolution 43:616-626.

93. Richter, S., J. Olesen, and W. C. Wheeler. 2007. Phylogeny of Branchiopoda (Crustacea) based on a combined analysis of morphological data and six molecular loci. Cladistics 23:301-336.

92. Arango, C. A., and W. C. Wheeler. 2007. Phylogeny of the sea spiders (Arthropoda, Pycnogonida) based on direct optimization of six loci and morphology. Cladistics 23:255-293.

91. Ramirez, M. J., J. Coddigton, W. P. Maddison, P. Midford, L. Prendini, J. Miller, C. E. Griswold, G. Hormiga, P. Sierwald, N. Scharff, S. P. Benjamin, and W. C. Wheeler. 2007. Linking of digital images to phylogenetic data matrices using a morphological ontology: lesson from the AtoL:Phylogeny of Spiders project. Syst. Biol. 56:283-294.

90. Wheeler, W. C. 2007. “The analysis of molecular sequences in large data sets: where should we put our effort?” Pp. 113-128, In Trevor R. Hodkinson and John A. N. Parnell eds., Reconstructing the Tree of Life: Taxonomy and Systematics of Species Rich Taxa. Systematics Association, Oxford University Press.

89. Vinh, L., A. Varon, and W. C. Wheeler. 2006. Pairwise alignment with rearrangement. Genome Informatics 17(2):141-151.

88. Wheeler, W. C. Dynamic homology and the likelihood criterion. 2006. Cladistics 22:157-170.

87. Wheeler, W. C., M. J. Ramírez, L. Aagesen, and S. Schulmeister. 2006. Partition-Free Congruence Analysis: Implications for Sensitivity Analysis. Cladistics 22:26-263.

86. Grant, T., D.R. Frost, J.P. Caldwell, R. Gagliardo, C.F.B. Haddad, P.J.R. Kok, B.D. Means, B.P. Noonan, W. Schargel, and W.C. Wheeler. 2006. Phylogenetic systematics of dart-poison frogs and their relatives (Anura: Athesphatanura: Dendrobatidae). Bulletin of the American Museum of Natural History 299:184-203.

85. Frost, D. R., T. Grant, J. Faivovich, A. Haas, C. F. B. Haddad, R. Bain, R. O. de Sá, S. C. Donnellan, C. J. Raxworthy, M. Wilkinson, A. Channing, J. A. Campbell, B. L. Blotto, P. Moler, R. C. Drewes, R. A. Nussbaum, J. D. Lynch, D. Green and W. C. Wheeler. 2006. The amphibian tree of life. Bulletin of the American Museum of Natural History 297: 1-370.

84. Pickett, K. M., J. M. Carpenter, and W. C. Wheeler. 2006. A systematic update  of Polistes (Hymenoptera: Vespidae), with phylogenetic consideration  of social behavior. Annales Zoologici Finnici 43:390-406.

83. Smith, W. L. and Wheeler, W. C. 2006. Venom evolution widespread in fishes: A phylogenetic roadmap for the bioprospecting of piscine venoms. J. Heredity 97:206-217.

82. Picket, K. M., G. L. Tolman, W. C. Wheeler, and J. W. Wenzel. 2005. Parsimony overcomes statistical inconsistency with the addition of more data from the same gene. Cladistics 21:438-445.

81. Prendini, L. and W. C. Wheeler. 2005. Scorpion higher phylogeny and classification, taxonomic anarchy, and standards for peer review in online publishing. Cladistics 21:446-494.

80. Ogden, T. H., M. F. Whiting, and W. C. Wheeler. 2005. Poor taxon sampling, poor character sampling, and non-repeatable analyses of a contrived dataset do not provide a more credible estimate of insect phylogeny: a reply to Kjer. Cladistics 21:295-302.

79. Prendini, L., Weygoldt, P. and Wheeler, W.C. 2005. Systematics of the Damon variegatus group of African whip spiders (Chelicerata: Amblypygi):Evidence from behaviour, morphology and DNA. Organisms, Diversity and Evolution, 5:203-236.

78. Wheeler, W. C. 2005. “Alignment, Dynamic Homology, and Optimization.” Pp. 71-80 in Parsimony, Phylogeny, and Genomics. V. A. Albert eds. Oxford University Press, Oxford.

77. Faivovich, J.; Haddad, C. F. B.; Garcia, P. C. A.; Frost, D. R.; Campbell, J. A., and Wheeler, W. C., 2005. Systematic review of the frog family Hylidae, with special reference to Hylinae: Phylogenetic analysis and taxonomic revision. Bulletin of the American Museum of Natural History 294: 1- 240.

76. Giribet G, Richter, S., Edgecombe G. D, and Wheeler W.C. 2005. “The position of crustaceans within the Arthropoda—evidence from nine molecular loci and morphology.” Pp307-352 in Crustacea and Arthropod Relationships, S. Koenemann and R. A. Jenner eds. Taylor and Francis, Boca Raton.

75. Giribet G, Edgecombe G. D., Carpenter J.M., d‘Haese C., Wheeler W.C. 2004. Is Ellipura monophyletic? A combined analysis of basal hexapod relationships with emphasis on the origin of insects. Organisms, Diversity, and Evolution, 4:319-340.

74. Smith, W. L., and W. C. Wheeler. 2004. Polyphyly of the mail-cheeked fishes (Teleostei: Scorpaeniformes): evidence from mitochondrial and nuclear sequence data, Mol. Phyl. Evol., 32:627-646.

73. Favovich, J., P. C. A. Garcia, F. Ananias, L. Lanari, N. G. Basso, and W.C. Wheeler. 2004. A molecular perspective on the phylogeny of the Hyla pulchella species group (Anura: Hylidae). Mol. Phyl. Evol, 32:938-950.

72. Wheeler, W. C., G. Giribet, and G. D. Edgecombe. 2004. “Arthropod Systematics: The Comparative Study of Genomic, Anatomical, and Paleontological Information.” pp. 281-295, Assembling the Tree of Life. J. Cracraft and M. J. Donoghue eds. Oxford University Press, Oxford.

71. Wheeler, W. C., D. Janies, and J. De Laet. 2004. “DNA sequence alignment and parallel processing.” Pp 247-250, 2004 McGraw-Hill Yearbook of Science & Technology.

70. Schulmeister, D. and W. C. Wheeler. 2004. Comparative and Phylogenetic analysis of developmental sequences. Evolution and Development, 6:50-57.

69. Wheeler, W. C. 2003. Search-Based Optimization. Cladistics, 19:348-355.

68. Wheeler, W. C. 2003. Implied Alignment: A Synapomorphy-Based Multiple Sequence Alignment Method. Cladistics, 19:261-268.

67. Wheeler, W. C. 2003. Iterative pass optimization. Cladistics, 19:254-260.

66. Norell, M. A., and W. C. Wheeler. 2003. Missing entry replacement data analysis: a statistical approach to dealing with missing data in paleontological and total evidence data sets. J. Vert. Paleont. 23:275-283.

65. Prendini, L., Crowe, T.M., and Wheeler, W.C. 2003. The family Scorpionidae Latreille, 1802: Phylogeny, taxonomy and biogeography. Invertebrate Systematics, 17:185-259.

64. Wheeler, W. C. 2002. “Optimization Alignment: Down, Up, Error, and Improvements.” Pp. 55-69. in R. Desalle, G. Giribet and W. Wheeler eds. Techniques in Molecular Systematics and Evolution. Birkhäuser Verlag, Basel Switzerland.

63. Wheeler, W. C., G. Giribet, and G. D. Edgecombe. 2002. “Arthropods.” Pp74-77, In Encyclopedia of Evolution, Mark Pagel ed.. Oxford University Press.

62. Girbet, G., and W. C. Wheeler. 2002. On bivalve phylogeny: a high-level phylogeny of the mollusk class Bivalvia based on a combined analysis of morphology and DNA sequence data. Inv. Biol 121:271-324.

61. Janies, D. and W. C. Wheeler. 2002. “Theory and practice of parallel direct optimization.” pp. 115-124 in R. Desalle, G. Giribet and W. Wheeler eds. Molecular Systematics and Evolution: Theory and Practice. Birkhäuser Verlag, Basel Switzerland.

60. Edgecombe, G. D., G. Giribet, and W. C. Wheeler. 2002. Phylogeny of Henicopidae (Chilopoda: Lithobiomorpha): A combined analysis of morphology and five molecular loci. Syst. Ent.27:31-64.

59. Giribet, G., R. DeSalle, and W. C. Wheeler. 2002. “Pluralism” and the aims of phylogenetic analysis.” pp. 141-146 in R. Desalle, G. Giribet and W. Wheeler eds. Molecular Systematics and Evolution: Theory and Practice. Birkhäuser Verlag, Basel Switzerland.

58. Giribet, G., W. C. Wheeler, G. D. Edgecombe, and C. Babbitt. 2002. Phylogeny and systematic position of Opiliones: a combined analysis of chelicerate relationships using morphological and molecular data. Cladistics, 18:5-70.

57. Giribet, G., W. C. Wheeler, and J. Muona. 2002. “DNA multiple sequence alignments.” pp107-114 in R. Desalle, G. Giribet and W. Wheeler eds. Molecular Systematics and Evolution: Theory and Practice. Birkhäuser Verlag, Basel Switzerland.

56. Schulmeister, S., Wheeler, W. C., and Carpenter, J. M. 2002. Simultaneous analysis of basal Hymenoptera (Insecta) using sensitivity analysis. Cladistics 18:455-484.

55. Wheeler, W. C. 2001. “Homology and DNA sequence data.” Pp. 303-318. in G.P. Wagner ed. The Character Concept in Evolutionary Biology. Academic Press, New York. 622 pp.

54. Wheeler, W. C. 2001. Homology and the optimization of DNA sequence data. Cladistics, 17:S3-S11.

53. Wheeler , W. C., M. F. Whiting, J. C. Carpenter, and Q. D. Wheeler. 2001. “The phylogeny of the insect orders.” Cladistics, 12:1-57.

53a. Wheeler , W. C., M. F. Whiting, J. C. Carpenter, and Q. D. Wheeler. 2001. “The phylogeny of the insect orders.” Cladistics, 12:1-57. Erratum

52. Giribet, G and W. C. Wheeler. 2001. “Some unusual small-subunit ribosomal DNA sequences of metazoans.” AMNH Novitates., 3337:1-14.

51. Janies, D., and W. Wheeler. 2001. Efficiency of parallel direct optimization. Cladistics, 17:S71-S82.

50. Giribet, G., G. D. Edgecombe, and W. C. Wheeler. 2001. Arthropod phylogeny based on eight molecular loci and morphology. Nature 413: 157-161.

49. Giribet, G., W. Wheeler, and D. Janies. 2001. Introduction. Cladistics 17:S1-S2.

48. Giribet, G., D. L. Distel, M. Polz, W. Sterrer, and W. C. Wheeler. 2000. “Triploblastic relationships with emphasis on the acoelomates, and the position of Gnathostomulida, Cycliophora, Platyhelminthes, and Chaetognatha; a combined approach of 18S rDNA and Morphology.” Systematic Biology, 49:539-562.

47. Phillips, A., D. Janies, and W. C. Wheeler. 2000. “Multiple sequence alignment in phylogenetic analysis.” Mol. Phyl. Evol. 16:317-330.

46. Wheeler, W. C. 2000. Heuristic Reconstruction of Hypothetical-Ancestral DNA Sequences: Sequence Alignment versus Direct Optimization. Pp. 106-113. in R. Scotland and R. T. Pennington eds. Homology and Systematics. Systematics Society, London. 217 pp.

45. Bang, R., R. DeSalle, and W. C. Wheeler. 2000. “Transformationalism, taxism and the role of developmental biology in systematics.” Sys. Biol, 49:19-27.

44. Edgecombe, G. D., Gonzalo Giribet and Ward Wheeler. 1999. “Phylogeny of Chilopoda: combining 18s and 28s rDNA sequences and morphology.” Pp. 293-331. in Evolución y filogenia de Arthropoda (A. Melic, ed.). Sociedad Entomológica Aragonesa.

43. Giribet, G., G. D. Edgecombe, y W. C. Wheeler. 1999. “Sistemática y Filogenia de Artrópodos; estado de la cuestión con énfasis en análisis de datos moleculares.” Pp197-212. in Evolución y filogenia de Arthropoda (A. Melic, ed.). Sociedad Entomológica Aragonesa.

42. Carpenter, J. M., and W. C. Wheeler. 1999. “Numerical Cladistics, Simultaneous Analysis and Hexapod Phylogeny.” Pp 333-346, in Evolución y filogenia de Arthropoda (A. Melic, ed.). Sociedad Entomológica Aragonesa.

41. Wheeler, W. C. 1999. “Fixed Character States and the Optimization of Molecular Sequence Data.” Cladistics 15: 379-385.

40. Wheeler, W. 1999. “Measuring topological congruence by extending character techniques.” Cladistics, 15:131-135.

39. Carpenter, J. M. and W. C. Wheeler. 1999. “Towards simultaneous analysis of morphological and molecular data in Hymenoptera.” Zoologica Scripta 28:251-260.

38. Giribet, G and W. C. Wheeler. 1999. “The position of arthropods in the animal kingdom: Ecdysozoa, islands, trees and the ‘parsimony ratchet.’” Molecular Phylogenetics and Evolution, 10:1-5.

37. Giribet, G and W. C. Wheeler. 1999. “On Gaps.” Molecular Phylogenetics and Evolution, 13:132-143.

36. Wheeler, W. C. 1998. “Alignment Characters, Dynamic Programming, and Heuristic Solutions” pp. 243-251 in R. DeSalle, B. Schierwater, eds. Molecular Approaches to Ecology and Evolution 2nd Edition. Birkhäuser Verlag, Basel Switzerland.

35. Wheeler, W. C. 1998. “Molecular systematics and Arthropods.” Pp. 9-32. in G. D. Edgecombe ed. Arthropod Fossils and Phylogeny, Columbia University Press, New York.

34. Wheeler, W. C. and C. Y. Hayashi. 1998. “The phylogeny of the extant chelicerate orders.” Cladistics 14:173-192.

33. Wheeler, W. C. 1998. “Sampling, groundplans, total evidence and the systematics of arthropods.” Pp. 87-96. in R. A. Fortey and R. H. Thomas eds. Arthropod Relationships. Chapman and Hall, London.

32. Gladstein, D. S. and W. C. Wheeler. 1997-2000. “POY: The Optimization of Alignment Characters.” Program and Documentation. New York, NY. Available at Documentation by D. Janies and W. C. Wheeler.

31. Whiting, M. F., J. C. Carpenter, Q. D. Wheeler, and W. C. Wheeler. 1997. “The Strepsiptera problem: phylogeny of the holometabolous insect orders inferred from 18S and 28S ribosomal DNA sequences and morphology.” Syst. Biol. 46:1-68.

30. Wheeler, W. C. 1996. “Optimization Alignment: the end of multiple sequence alignment in phylogenetics?” Cladistics, 12:1-9.

29. Vrana, P. B. and W. C. Wheeler. 1996. “Molecular evolution and phylogenetic utility of the Polyubiquitin locus in mammals and higher vertebrates.” Mol. Phyl. and Evol., 6:259-269.

28. Wheeler, W. C. 1995. “Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data.” Systematic Biology 44:321-331.

27. Wheeler, W. C., J. Gatesy, and R. DeSalle. 1995. “Elision: a method for accommodating multiple molecular sequence alignments with alignment-ambiguous sites.” Mol. Phyl. Evol.4:1-9.

26. Farris, J. S., 28 others, and W. Wheeler. 1995. “Explanation.” Cladistics 11:211-218.

25. Wheeler, W. C. 1994. “Sources of ambiguity in nucleic acid sequence alignment.” pp. 323-352 in B. Schierwater, B. Streit, G.P. Wagner, and R. DeSalle eds. Molecular Ecology and Evolution: Approaches and Applications. Birkhäuser Verlag, Basel Switzerland

24. Wheeler, W. C., and D. S. Gladstein. 1994. “MALIGN: A multiple sequence alignment program.” J. Hered. 85:417-418.

23. Wheeler, W. C., and K. Nixon. 1994. “A novel method for the economical diagnosis of cladograms under Sankoff optimization.” Cladistics 10:207-213.

22. Whiting, M., and W. C. Wheeler. 1994. “Insect homeotic transformation.” Nature, 368:696.

21. Vrana, P. B., M. C. Milinkovitch, J. R. Powell, and W. C. Wheeler. 1994. “Higher level relationships of the arctoid Carnivora based on sequence data and ‘total evidence’.”Mol. Phyl. Evol. 3:47-58.

20. Wheeler, W. C. 1993. “The triangle inequality and character analysis.” Mol. Biol. and Evol. 10:707-712.

19. Wheeler, W. C., R. T. Schuh, and R. Bang. 1993. “Cladistic relationships among higher groups of Heteroptera: congruence between morphological and molecular data sets.” Ent. Scand., 24:121-138

18. Wheeler, W. C., P. Cartwright, and C. Y. Hayashi. 1993. “Arthropod phylogeny: a combined approach.” Cladistics 9:1-39.

17. DeSalle, R., J. Gatesy, W. Wheeler, and D. Grimaldi. 1993. “Working with fossil DNA from amber.” Discovery, 24:19-21.

16. Dick, M., D. M. Bridge, W. C. Wheeler, and R. DeSalle. 1993. “Collection and storage of invertebrate samples.” Methods. Enzymol. 224:51-65.

15. Gatesy, J., R. DeSalle, and W. Wheeler. 1993. “Alignment-ambiguous nucleotide sites and the exclusion of systematic data.” Mol. Phyl. Evol., 2:152-157.

14. Wheeler, W. C. 1992. “Quo vadis?” Cladistics 8:85-86.

13. Wheeler, W. C. 1992. “Extinction, sampling, and molecular phylogenetics.” pp. 205-215 in M. Novacek and Q. D. Wheeler, eds. Extinction and Cladistic Analysis. Columbia University Press, New York.

12. Wheeler, W. C. and D. S. Gladstein. 1991-1998. MALIGN. Program and documentation. New York, NY. Documentation by Daniel Janies and Ward Wheeler.

11. Vrana, P., and W. C. Wheeler. 1992. “Individual organisms as terminal entities: laying the species problem to rest.” Cladistics 8:67-72.

10. DeSalle, R., J. Gatesy, W. Wheeler, and D. Grimaldi. 1992. “DNA sequences from a fossil termite in Oligo-Miocene amber and their phylogenetic implications.” Science 257:1933-1936.

9. Wheeler, W. C. 1991. “Congruence among data sets: a Bayesian approach.” pp 334-346 in M. M. Miyamoto and J. Cracraft, eds. Phylogenetic Analysis of DNA Sequences. Oxford University Press, London.

8. Wheeler, W. C. 1990. “Nucleic acid sequence phylogeny and random outgroups.” Cladistics 6:363-367.

7. Wheeler, W. C. 1990. “Invertebrate relationships.” Journal of the New York Ent. Soc. 98:502-504.

6. Wheeler, W. C. 1990. “Combinatorial weights in phylogenetic analysis: a statistical parsimony procedure.” Cladistics 6:269-275.

5. Honeycutt, R. L., and W. C. Wheeler. 1990. “Mitochondrial DNA: Variation in Humans and Higher Primates.” in CRC Press, DNA Systematics in Humans and Higher Primates. pp. 91-129.

4. Wheeler, W. C. 1989. “The systematics of insect ribosomal DNA.” in The Hierarchy of Life. Bö Fernholm et al. eds. Elsevier Press, Amsterdam. pp. 307-321.

3. Wheeler, W. C., and R. L. Honeycutt. 1988. “Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications.” Mol. Biol. and Evol. 5:90-96.

2. Harrison, R. G., D. M. Rand, and W. C. Wheeler. 1987. “Mitochondrial DNA variation in field crickets across a narrow hybrid zone.” Molec. Biol. and Evol. 4:144-158.

1. Harrison, R. G., D. M. Rand, and W. C. Wheeler. 1985. “Mitochondrial DNA heteroplasmy within individual crickets.” Science 228:1446-1448.

Edited Volumes
2. R. Desalle, G. Giribet and W. Wheeler. 2002. Techniques in Molecular Systematics and Evolution. Birkhäuser Verlag, Basel Switzerland, 450 pp.

1. R. Desalle, G. Giribet and W. Wheeler. 2002. Molecular Systematics and Evolution: Theory and Practice. Birkhäuser Verlag, Basel Switzerland. 309 pp.

Authored Volumes
2. Wheeler, W. C. Systematics: A Course of Lectures. J. Wiley, 2012. 426pp.

1. Wheeler, W. C., L. Aagesen, C. P. Arango, J. Faivovich, T. Grant, C. D’Haese, D. Janies, W. L. Smith, A. Varon, and G. Giribet. Dynamic Homology and Phylogenetic Systematics: a Unified Approach Using POY. 2006. American Museum Novitates. Pp 445.

Technical Notes
1. Varón, A., W. C.Wheeler, and A. Bar-Noy. 2008. An efficient heuristic for the Tree Alignment problem. Dec. 18, 2008.


5. Wheeler, W. C., N. Lucaroni. L. Hong, L. M. Crowley, and A. Varón. 2013. POY 5.0. American Museum of Natural History.

4. Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0. American Museum of Natural History.

3. Wheeler, W. C., D. S. Gladstein, and Jan De Laet. 2002-2003. POY. Version 3.0. /pub/molecular/poy. Documentation by Daniel Janies and Ward Wheeler. Commandline documentation by J. De Laet and W. C. Wheeler.

2. Wheeler, W. C., and D. S. Gladstein. 1996-2001. POY. Version 2.0. /pub/molecular/poy.

1. Wheeler, W. C. and D. S. Gladstein. 1991-1998. MALIGN. Program and documentation. New York, NY. Documentation by Daniel Janies and Ward Wheeler.