Education
1985 to 1988 Harvard University Ph. D.
1981 to 1985 Yale College B. A.

Adjunct Appointments
1991 to present Adjunct Professor, Columbia University
1991 to present Adjunct Professor, New York University
1989 to present Adjunct Professor, City University of New York

Software
• Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2007. POY 4.0 Beta 2398. Documentation by A. Varón, L. S. Vinh, I. Bomash, W. Wheeler, K. Pickett, I. Tëmkin, J. Faivovich, T. Grant, and W. L. Smith. Available for download at http://research.amnh.org/scicomp/projects/poy.php.

• Wheeler, W. C., D. S. Gladstein, and Jan De Laet. 1996-2003. POY. Version 3.0. ftp.amnh.org /pub/molecular/poy (current version 3.0.11). Documentation by Daniel Janies and Ward Wheeler. Commandline documentation by J. De Laet and W. C. Wheeler.

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

Publications
Reprints may be downloaded by clicking on each reference. In doing so, you agree to comply with United States copyright law (Title 17, United States Code), such that the reprints are not to be "used for any purpose other than private study, scholarship, or research."

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

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.

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.

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

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. Vari10, 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.

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. 2007. Is The Amphibian Tree of Life really fatally flawed? Cladistics 23:1-11.

Le Sy, V., 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.

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.

Pellenes, 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.

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.

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.

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.

Vinh, L. S., A. Varón, and W. C. Wheeler. 2006. Pairwise alignment with rearrangement. Genome Informatics 17:141-151.

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

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: 1-262.

Wheeler, W.C. , M.J. Ramírez, L. Aagesen, and S. Schulmeister. 2006. Partition-free congruence analysis. Cladistics 22: 256-263.

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

Frost, D.R., T. Grant, J. Faivovich, R. Bain, A. Haas, C.F.B. Haddad, 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.

Pickett, 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.

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

Wheeler, W. C. 2005. “Alignment, Dynamic Homology, and Optimization.” pp71-80 in Parsimony, Phylogeny, and Genomics. V. A. Albert eds. Oxford University Press, Oxford.

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.

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

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.

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.

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.

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.

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

Schulmeister, D. and W. C. Wheeler. 2004. Phylogenetic analysis of developmental sequence heterochrony: an application of search-based character optimization. Evolution and Development, 6:50-57.

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

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

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

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.

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

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.

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

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.

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.

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.

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.

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.

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.

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

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.

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

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

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

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

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

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.

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

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 Sytematics. Systematics Society, London. 217 pp.

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

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.

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.” In: Evolución y filogenia de Arthropoda (A. Melic, ed.). Sociedad Entomológica Aragonesa.

Carpenter, J. M., and W. C. Wheeler. 1999. “Numerical Cladistics, Simultaneous Analysis and Hexapod Phylogeny.” In: Evolución y filogenia de Arthropoda (A. Melic, ed.). Sociedad Entomológica Aragonesa.

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

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

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

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.

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

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.

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.

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

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.

Gladstein, D. S. and W. C. Wheeler. 1997-2002. “POY: The Optimization of Alignment Characters.” Program and Documentation. New York, NY. Available at ftp.amnh.org/pub/molecular. Documentation by D. Janies and W. C. Wheeler.

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.

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

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.

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

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.

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

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

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

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

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

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.

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

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.

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

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

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

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

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

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.

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

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

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.

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.

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

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

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

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.

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.

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.

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.

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

Authored Volumes
Wheeler, W.C. , L. Aagesen, C. P. Arango, J. Faivovich, T. Grant, C. D'Haese, D. Janies, W. L. Smith, A. Varón, and G. Giribet. 2006. Dynamic Homology and Phylogenetic Systematics: A Unified Approach Using POY. American Museum of Natural History, New York. 365 pp.

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

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