Computational Sciences: Publications
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Acknowledgements
Please acknowledge the The American Museum of Natural History shared Cluster Computing facility and staff in publications (refereed, dissertations, theses, etc.), presentation, and reports, which have in any way benefited from the availability of these resources. One way to acknowledge the facility and staff is by including the following statement in your publications:
We acknowledge the American Museum of Natural History shared Cluster Computing facility and staff for contributions to results presented in this paper.
Publications
Empirical and theoretical papers in astrophysics and biological sciences are listed in reverse chronological order, and 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. , 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.
Vinh, L. S., A. Varón, and W. C. Wheeler. 2006. Pairwise alignment with rearrangement. Genome Informatics 17(2):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.
Jansen, G., S. Devaere, P.H.H. Weekers, and D. Adriaens. 2006. Phylogenetic relationships and divergence time estimate of African anguilkliform catfish (Siluriformes: Clariidae) inferred from ribosomal gene and spacer sequences. Molecular Phylogenetics and Evolution 38: 65-78.
Schelly, R., W. Salzburger, S. Koblmuller, N. Duftner, and C. Sturmbauer. 2006. Phylogenetic relationships of the lamprologine cichlid genus Lepidiolamprologus (Teleostei: Perciformes) based on mitochondrial and nuclear sequences, suggesting introgressive hybridization. Molecular Phylogenetics and Evolution 38: 426-438.
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.
Aagesen, L. 2005. Direct optimization, affine gap costs, and node stability. Molecular Phylogenetics and Evolution 36: 641-653.
Aagesen, L., G. Petersen, and O. Seberg. 2005. Sequence length variation, indel costs, and congruence in sensitivity analysis. Cladistics 21: 15-30.
Prendini, L., P. Weygoldt, and W.C. Wheeler. 2005. Systematics of the Damon variegatusgroup of African whip spiders (Chelicerata: Amblypygi): Evidence from behaviour, morphology and DNA. Organisms Diversity & Evolution 5: 203-236.
Brito, P.H. 2005. The influence of Pleistocene glacial refugia on tawny owl genetic diversity and phylogeography in western Europe. Molecular Ecology 14: 3077-3094.
Wheeler, W. C. 2005. “Alignment, Dynamic Homology, and Optimization.” pp71-80 in Parsimony, Phylogeny, and Genomics. V. A. Albert eds. Oxford University Press, Oxford.
Sparks, J.S., P.V. Dunlap, and W.L. Smith. 2005. Evolution and diversification of a secually dimorphic luminescent system in ponyfishes (Teleostei: Leiognathidae), including diagnoses for two new genera. Cladistics 21: 305-327.
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.” Pp. 307-352 in Crustacea and Arthropod Relationships, S. Koenemann and R. A. Jenner eds. Taylor and Franscis, Boca Raton.
Sparks, J.S., and W.L. Smith. 2004a. Phylogeography and biogeography of cichlid fishes (Teleostei: Perciformes: Cichlidae). Cladistics 20: 501-517.
Sparks, J.S., and W.L. Smith. 2004b. Phylogeny and biogeography of the Malagasy and Australian rainbowfishes (Teleostei: Melanotaenioidei): Gondwanan vicariance and evolution in freshwater. Mol. Phyl. Evol. 33: 719-734.
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.
Faivovich, 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.
Asher, R.J., I. Horovitz, and M.R. Sanchez-Villagra. 2004. First combined cladistic analysis of marsupial mammal interrelationships. Molecular Phylogenetics and Evolution 33: 240-250.
Wheeler, W. C. 2003. Search-Based Optimization. Cladistics, 19:348-355.
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.
Asher, R.J., M.J. Novacek, and J.H. Geisler. 2003. Relationships of endemic African mammals and their fossil relatives based on morphological and molecular evidence. Journal of Mammalian Evolution 10: 131-164.
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.
Frost, D.R., D. Janies, P.l.F. Mouton, and T.A. Titus. 2001. A molecular perspective on the phylogeny of the girdles lizards (Chordylidae, Squamata). American Museum Novitates 3310: 1–10.
Frost, D.R., M.T. Rodrigues, T. Grant, and T.A. Titus. 2001. Phylogenetics of the lizard genus Tropidurus (Squamata: Tropiduridae: Tropidurinae): Direct optimization, descriptive efficiency, and sensitivity analysis of congruence between molecular data and morphology. Molecular Phylogenetics and Evolution 21: 352–371.
Frost, D.R., R. Etheridge, D. Janies, and T.A. Titus. 2001. Total evidence, sequence alignment, evolution of polychrotid lizards, and a reclassification of the Iguania (Squamata: Iguania). American Museum Novitates 3343: 1–38.
Giribet, G and W. C. Wheeler. 2001. Some unusual small-subunit ribosomal DNA sequences of metazoans. American Museum Novitates., 3337:1-14.
Janies, D., and W. Wheeler. 2001. Efficiency of parallel direct optimization. Cladistics, 17:S71-S82.
Janies, D. 2001. Phylogenetic relationships of extant echinoderm classes. Canadian Journal of Zoology 79: 1232–1250.
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.
Janies, D., and R. Mooi. 1998. Xyloplax is an asteroid. In M. Candia Carevali, and F. Bonasoro (eds), Echinoderm Research 1998. A. A. Balkema, Rotterdam, Netherlands, pp. XX–XX.
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.