Phylogenetic utility of dynamin and triose phosphate isomerase

Systematic Entomology

Volumn 32, Issue 2, 2007, Pages 396-403

  Hardy, Nate B ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMARKER; INSECT; PHYLOGENETICS; POLYMERASE CHAIN REACTION;

COCCOIDEA; HEMIPTERA; HEXAPODA;

EID: 34247472240     PISSN: 03076970     EISSN: 13653113     Source Type: Journal    
DOI: 10.1111/j.1365-3113.2007.00377.x     Document Type: Article

References (37)

1. Beltrán, M., Jiggins, C.D., Bull, V., Linares, M., Mallet, J., McMillan, W.O. & Bermingham, E. (2002) Phylogenetic discordance at the species boundary: comparative gene genealogies among rapidly radiating Heliconius butterflies. Molecular Biology and Evolution, 19, 2176-2190.
2. Blum, M.J., Bermingham, E. & Dasmahapatra, K. (2003) A molecular phylogeny of the neotropical butterfly genus Anartia (Lepidoptera: Nymphalidae). Molecular Phylogenetics and Evolution, 26, 46-55.
3. Brandley, M.C., Schmitz, A. & Reeder, T.W. (2005) Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scinid lizards. Systematic Biology, 54, 373-390.
4. Brown, J.R., Daar, I.O., Krug, J.R. & Maquat, L.E. (1985) Characterization of the functional gene and several processed pseudogenes in the human triosephosphate isomerase gene family. Molecular and Cellular Biology, 5, 1694-1706.
5. Cook, L.G. & Gullan, P.J. (2004) The gall-inducing habit has evolved multiple times among the eriococcid scale insects (Sternorrhyncha: Coccoidea: Eriococcidae). Biological Journal of the Linnean Society, 83, 441-452.
6. Danforth, B.N., Lin, C. & Fang, J. (2005) How do insect nuclear ribosomal genes compare to protein-coding genes in phylogenetic utility and nucleotide substitution patterns? Systematic Entomology, 30, 549-562.
7. DeBry, R.W. (2001) Improving interpretation of the decay index for DNA sequence data. Systematic Biology, 50, 742-752.
8. von Dohlen, C.D. & Moran, N.A. (1995) Molecular phylogeny of the Homoptera: a paraphyletic taxon. Journal of Molecular Evolution, 41, 211-223.
9. Don, R.H., Cox, P.T., Wainwright, B.J., Baker, K. & Mattick, J.S. (1991) 'Touchdown' PCR to circumvent spurious priming during gene amplification. Nucleic Acids Research, 19, 4008.
10. Downie, D.A. & Gullan, P.J. (2004) Phylogenetic analysis of mealybugs (Hemiptera: Coccoidea: Pseudococcidae) based on DNA sequences from three nuclear genes, and a review of the higher classification. Systematic Entomology, 29, 238-259.
11. Dowton, M. & Austin, A.D. (1998) Phylogenetic relationships among the microgastroid wasps (Hymenoptera: Braconidae): combined analysis of 16S and 28S rDNA genes and morphological data. Molecular Phylogenetics and Evolution, 10, 354-366.
12. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792-1797.
13. Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783-791.
14. Gilbert, W., Marchionni, M. & McKnight, G. (1986) On the antiquity of introns. Cell, 46, 151-154.
15. Gullan, P.J., Downie, D.A. & Steffan, S.A. (2003) A new pest species of the mealybug genus Ferrisia Fullaway (Hemiptera: Pseudococcidae) from the United States. Annals of the Entomological Society of America, 96, 723-737.
16. Gullan, P.J., Miller, D.R. & Cook, L.G. (2004) Gall-inducing scale insects (Hemiptera: Sternorrhyncha: Coccoidea). Biology, Ecology and Evolution of Gall-inducing Arthropods (ed. by A. Raman, C.W. Schaefer and T.M. Withers), pp. 195-196. Science Publishers, Enfield.
17. Kass, R.E. & Raftery, A.E. (1995) Bayes factors. Journal of the American Statistical Association, 90, 773-795.
18. Kolaczkowski, B. & Thornton, J.W. (2004) Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature, 431, 980-984.
19. Lolis, E., Alber, T., Davenport, R.C., Rose, D., Hartman, F.C. & Petsko, G.A. (1990) Structure of yeast triosephosphate isomerase at 1.9-A resolution. Biochemistry, 29, 6609-6618.
20. Maddison, W.P. & Maddison, D.R. (2002) Macclade, version 4.05. Sinauer Associates, Sunderland, MA.
21. Morse, G.E. & Normark, B.B. (2006) A molecular phylogenetic study of armoured scale insects (Hemiptera: Diaspididae). Systematic Entomology, 31, 338-349.
22. Nylander, J.A.A., Ronquist, F., Huelsenbeck, J.P. & Nieves-Aldrey, J.L. (2004) Bayesian phylogenetic analysis of combined data. Systematic Biology, 53, 47-67.
23. Peterson, K.J., Lyons, J.B., Nowak, K.S., Takacs, C.M., Wargo, M.J. & McPeek, M.A. (2004) Estimating metazoan divergence times with a molecular clock. Proceedings of the National Academy of Sciences, 101, 6536-6541.
24. Posada, D. & Crandall, K.A. (1998) Modeltest: testing the model of DNA substitution. Bioinformatics, 14(9), 817-818.
25. Regier, J.C. (2005) Protocols, concepts, and reagents for preparing DNA sequencing templates, version 4/01/05 (www.umbi.umd.edu/jcrlab/PCR_primers.pdf).
26. Regier, J.C. & Shi, D. (2005) Increased yield of PCR product from degenerate primers with nondegenerate, nonhomologous 59′-tails. Biotechniques, 38, 34, 36, 38.
27. Rogers, J. & Wall, R. (1980) A mechanism for RNA splicing. Proceedings of the National Academy of Sciences, 77, 1877-1879.
28. Rokas, A., King, N., Finnerty, J. & Carroll, S.B. (2003a) Conflicting phylogenetic signals at the base of the metazoan tree. Evolution and Development, 5, 346-359.
29. Rokas, A., Williams, B.L., King, N. & Carroll, S.B. (2003b) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature, 425, 798-804.
30. Ronquist, F. & Huelsenbeck, J.P. (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574.
31. Soltis, D.E., Albert, V.A., Savolainen, V. et al. (2004) Genome-scale data, angiosperm relationships, and 'ending incongruence': a cautionary tale in phylogenetics. Trends in Plant Science, 9, 477-483.
32. Sorenson, M.D. (1999) Treerot, version 2. Boston University, Boston.
33. Struck, T.H., Purschke, G. & Halanych, K.M. (2006) Phylogeny of Eunicida (Annelida) and exploring data congruence using a partition addition bootstrap alteration (PABA) approach. Systematic Biology, 55, 1-20.
34. Sweitzer, S.M. & Hinshaw, J.E. (1998) Dynamin undergoes a GTP-dependent conformational change causing vesiculation. Cell, 93, 1021-1029.
35. Swofford, D.L. (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods), version 4. Sinauer Associates, Sunderland, MA.
36. Tittiger, C., Whyard, S. & Walker, V.K. (1992) A novel intron site in the triosephosphate isomerase gene from the mosquito Culex tarsalis. Nature, 361, 470-472.
37. Whiting, M.F., Carpenter, J.C., Wheeler, Q.D. & Wheeler, W.C. (1997) The Strepsiptera problem: phylogeny of the holometabolous insect orders inferred from 18s and 28s ribosomal DNA sequences and morphology. Systematic Biology, 46, 1-68.