Identifying Conflicting Signal in a Multigene Analysis Reveals a Highly Resolved Tree: The Phylogeny of Rodentia (Mammalia)

Systematic Biology

Volumn 52, Issue 5, 2003, Pages 604-617

  DeBry, Ronald W ^a  

^a UNIVERSITY OF CINCINNATI   (United States)

Author keywords

Among site rate variation; Bayesian analysis; Likelihood ratio test; Maximum likelihood; Nucleotide substitution models; Partitioned analyses; Phylogeny; Rodentia

Indexed keywords

PRIMER DNA;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MONTE CARLO METHOD; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROBABILITY; REPRODUCIBILITY; RODENT; SPECIES DIFFERENCE; STATISTICAL MODEL;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; DNA PRIMERS; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MARKOV CHAINS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MONTE CARLO METHOD; PHYLOGENY; REPRODUCIBILITY OF RESULTS; RODENTIA; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

ANIMALIA; CASTORIDAE; DIPODIDAE; HYSTRICOGNATHI; MAMMALIA; MYOXIDAE; PEDETIDAE; RODENTIA;

EID: 0242487521     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150390235403     Document Type: Article

References (72)

1. ADKINS, R. M., E. L. GELKE, D. ROWE, AND R. L. HONEYCUTT. 2001. Molecular phylogeny and divergence time estimates for major rodent groups: Evidence from multiple genes. Mol. Biol. Evol. 18:777-791.
2. ADKINS, R. M., A. H. WALTON, AND R. L. HONEYCUTT. 2003. Higher-level systematics of rodents and divergence time estimates based on two highly congruent nuclear genes. Mol. Phylogenet. Evol. 26:409-420.
3. ANDERSON, S., AND J. K. JONES, JR. (eds.). 1984. Orders and families of Recent mammals of the world. Wiley, New York.
4. BUCKLEY, T. R. 2002. Model misspecification and probabilistic tests of topology: Evidence from empirical data sets. Syst. Biol. 51:509-523.
5. BUCKLEY, T. R., P. ARENSBURGER, C. SIMON, AND G. K. CHAMBERS. 2002. Combined data, Bayesian phylogenetics, and the origin of New Zealand cicada genera. Syst. Biol. 51:4-18.
6. BUCKLEY, T. R., C. SIMON, AND G. K. CHAMBERS. 2001. Exploring among-site rate variation models in a maximum likelihood framework using empirical data: Effects of model assumptions on estimates of topology, branch lengths, and bootstrap support. Syst. Biol. 50:67-86.
7. BUGGE, J. 1985. Systematic value of carotid arterial pattern in rodents. Pages 355-380 in Evolutionary relationships among rodents: A multidisciplinary analysis (W. P. Luckett and J.-L. Hartenberger, eds.). Plenum, New York.
8. BULL, J. J., J. P. HUELSENBECK, C. W. CUNNINGHAM, D. L. SWOFFORD, AND P. J. WADDELL. 1993. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42:384-397.
9. CHIPPINDALE, P. T., AND J. J. WIENS. 1994. Weighting, partitioning, and combining characters in phylogenetic analysis. Syst. Biol. 43:278-287.
10. CORBET, G. B. 1978. The mammals of the Palaearctic region: A taxonomic review. Cornell Univ. Press, Ithaca, New York.
11. CUNNINGHAM, C. W. 1997. Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods. Syst. Biol. 46:464-478.
12. DEBRY, R. W. 1999. Maximum likelihood analysis of gene-based and structure-based partitions, using mammalian mitochondrial genomes. Syst. Biol. 48:286-299.
13. DEBRY, R. W., AND R. M. SAGEL. 2001. Phylogeny of Rodentia (Mammalia) inferred from the nuclear-encoded gene IRBP. Mol. Phylogenet. Evol. 19:290-301.
14. DOWTON, M., AND A. D. AUSTIN. 2002. Increased congruence does not necessarily indicate increased phylogenetic accuracy - The behavior of the incongruence length difference test in mixed-model analyses. Syst. Biol. 51:19-31.
15. ELLERMAN, J. R. 1940. The families and genera of living rodents, Volumes 1 and 2. British Museum of Natural History, London.
16. FARRIS, J. S., M. KÄLLERSJÖ, A. G. KLUGE, AND C. BULT. 1994. Testing significance of incongruence. Cladistics 10:315-319.
17. GOLDMAN, N. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:182-198.
18. GOLDMAN, N., J. P. ANDERSON, AND A. G. RODRIGO. 2000. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49:652-670.
19. GU, X., Y. X. Fu, AND W.-H. LI. 1995. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol. Biol. Evol. 12:546-557.
20. HAFNER, M. S. 1982. A biochemical investigation of geomyoid systematics (Mammalia: Rodentia). Z. Zool. 20:118-139.
21. HARTENBERGER, J.-L. 1985. The order Rodentia: Major questions on their evolutionary origin, relationships, and suprafamilial systematics. Pages 1-33 in Evolutionary relationships among rodents: A multidisciplinary analysis (W. P. Luckett and J.-L. Hartenberger, eds.). Plenum, New York.
22. HUCHON, D., F. M. CATZEFLIS, AND E. J. P. DOUZERY. 1999. Molecular evolution of the nuclear von Willebrand factor gene in mammals and the phylogeny of rodents. Mol. Biol. Evol. 16:577-589.
23. HUCHON, D., F. M. CATZEFLIS, AND E. J. P. DOUZERY. 2000. Variance of molecular datings, evolution of rodents, and the phylogenetic affinities between Ctenodactylidae and Hystricognathi. Proc. R. Soc. Lond. B 267:393-402.
24. HUCHON, D., O. MADSEN, M. J. J. B. SIBBALD, K. AMENT, M. J. STANHOPE, F. CATZEFLIS, W. W. DE JONG, AND E. J. P. DOUZERY. 2002. Rodent phylogeny and a timescale for the evolution of Glires: Evidence from an extensive taxon sampling using three nuclear genes. Mol. Biol. Evol. 19:1053-1065.
25. HUELSENBECK, J. P., AND K. A. CRANDALL. 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Rev. Ecol. Syst. 28:437-466.
26. HUELSENBECK, J. P., AND F. RONQUIST. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754-755.
27. HUELSENBECK, J. P., D. L. SWOFFORD, C. W. CUNNINGHAM, J. J. BULL, AND P. J. WADDELL. 1994. Is character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis? Syst. Biol. 43:288-291.
28. JOW, H., C. HUDELOT, M. RATTRAY, AND P. G. HIGGS. 2002. Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution. Mol. Biol. Evol. 19:1591-1601.
29. KAFATOS, F. C., A. EFSTRATIADIS, B. G. FORGET, AND S. M. WEISSMAN. 1977. Molecular evolution of human and rabbit β-globin mRNAs. Proc. Natl. Acad. Sci. USA 74:5618-5622.
30. KISHINO, H., AND M. HASEGAWA. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29:170-179.
31. KLINGENER, D. 1984. Gliroid and dipodoid rodents. Pages 381-388 in Orders and families of Recent mammals of the world (S. Anderson and J. K. Jones, Jr., eds.). John Wiley and Sons, New York.
32. KLUGE, A. G., AND A. J. WOLF. 1993. Cladistics: What's in a word? Cladistics 9:183-199.
33. LAVOCAT, R., AND J.-P. PARENT. 1985. Phylogenetic analysis of middle ear features in fossil and living rodents. Pages 333-354 in Evolutionary relationships among rodents: A multidisciplinary analysis (W. P. Luckett and J.-L. Hartenberger, eds.). Plenum, New York.
34. LOCKHART, P. J., M. A. STEEL, M. D. HENDY, AND D. PENNY. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11:605-612.
35. LOVEJOY, N. R., AND B. B. COLLETTE. 2001. Phylogenetic relationships of New World needlefishes (Teleostei: Belonidae) and the biogeography of transitions between marine and freshwater habitats. Copeia 2001:324-338
36. LUCKETT, W. P., AND J.-L. HARTENBERGER. 1985. Evolutionary relationships among rodents: Comments and conclusions. Pages 685-712 in Evolutionary relationships among rodents: A multidisciplinary analysis (W. P. Luckett and J.-L. Hartenberger, eds.) Plenum, New York.
37. MCKENNA, M. C., AND S. K. BELL. 1997. Classification of mammals above the species level. Columbia Univ. Press, New York.
38. MONTGELARD, C., S. BENTZ, C. DOUADY, J. LAUQUIN, AND F. M. CATZEFLIS. 2002. Molecular systematics of Sciurognathi (Rodentia): The mitochondrial cytochrome b and 12S rRNA genes support the Anomaluroidea (Pedetidae and Anomaluridae). Mol. Phylogenet. Evol. 22:220-233.
39. MOUCHIROUD, D., C. GAUTIER, AND G. BERNARDI. 1995. Frequencies of synonymous substitutions in mammals are gene-specific and correlated with frequencies of nonsynonymous substitutions. J. Mol. Evol. 40:107-113.
40. MURPHY, W. J., E. EIZIRIK, W. E. JOHNSON, Y. P. ZHANG, O. A. RYDER, AND S. J. O'BRIEN. 2001a. Molecular phylogenetics and the origins of placental mammals. Nature 1409:614-618.
41. MURPHY, W. J., E. EIZIRIK, S. J. O'BRIEN, O. MADSEN, M. SCALLY, C. J. DOUADY, E. TEELING, O. A. RYDER, M. J. STANHOPE, W. W. DE JONG, AND M. S. SPRINGER. 2001b. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294:2348-2351.
42. NAYLOR, G. J. P., AND W. M. BROWN. 1997. Structural biology and phylogenetic estimation. Nature 388:527-528.
43. NEDBAL, M. A., R. L. HONEYCUTT, AND D. A. SCHLITTER. 1996. Higher-level systematics of rodents (Mammalia: Rodentia): Evidence from the mitochondrial 12S rRNA gene. J. Mamm. Evol. 3:201-237.
44. RAMBAUT, A., AND N. C. GRASSLY. 1997. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
45. RENSBERGER, J. M. 1971. Entoptychine pocket gophers (Mammalia: Geomyoidea) of the early Miocene John Day Formation, Oregon. Univ. Calif. Publ. Geol. Sci. 90:1-209.
46. RYAN, J. M. 1989. Comparative mycology and phylogenetic systematics of the Heteromyidae (Mammalia, Rodentia). Misc. Publ. Mus. Zool. Univ. Mich. 176:1-103.
47. SHIMODAIRA, H., AND M. HASEGAWA. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114-1116.
48. SHOTWELL, J. A. 1967. Late Tertiary geomyoid rodents of Oreg. Univ. Oregon Mus. Nat. Hist. Bull. 9:1-51.
49. SIMON, D., AND B. LARGET. 2000. Bayesian analysis in molecular biology and evolution (BAMBE), version 4.0 beta. Department of Mathematics and Computer Science, Duquesne Univ., Pittsburgh, Pennsylvania.
50. SIMPSON, G.G. 1945. The principles of classification and a classification of mammals. Bull. Am. Mus. Nat. Hist. 85:1-350.
51. STEEL, M. A., L. A. SZEKELY, AND M. D. HENDY. 1994. Reconstructing trees from sequences whose sites evolve at variable rates. J. Comp. Biol. 1:153-163.
52. SULLIVAN, J. 1996. Combining data with different distributions of among-site rate variation. Syst. Biol. 45:375-380.
53. SULLIVAN, J., AND D. L. SWOFFORD. 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. J. Mammal. Evol. 4:77-86.
54. SULLIVAN, J., AND D. L. SWOFFORD. 2001. Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated? Syst. Biol. 50:723-729.
55. SWOFFORD, D. L. 2001. PAUP *: Phylogenetic analysis using parsimony (* and other methods), version 4. Sinauer, Sunderland, Massachusetts.
56. SWOFFORD, D. L., G. J. OLSEN, P. J. WADDELL, AND D. M. HILLIS. 1996. Phylogenetic inference. Pages 407-514 in Molecular systematics, 2nd edition (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer, Sunderland, Massachusetts.
57. TEELING, E. C., O. MADSEN, R. A. VAN DEN BUSSCHE, W. W. DE JONG, M. J. STANHOPE, AND M. S. SPRINGER. 2002. Microbat paraphyly and the convergent evolution of a key innovation in Old World rhinolophoid microbats. Proc. Natl. Acad. Sci. USA 99:1431-1436.
58. TEELING, E. C., M. SCALLY, D. J. KAO, M. L. ROMAGNOLI, M. S. SPRINGER, AND M. J. STANHOPE. 2000. Molecular evidence regarding the origin of echolocation and flight in bats. Nature 403:188-192.
59. THOMPSON, J. D., D. G. HIGGINS, AND T. J. GIBSON. 1994. ClustalW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
60. THORNE J. L., N. GOLDMAN, AND D. T. JONES. 1996. Combining protein evolution and secondary structure. Mol. Biol. Evol. 13:666-673.
61. TICHER, A., AND D. GRAUR. 1989. Nucleic acid composition, codon usage, and the rate of synonymous substitution in protein-coding genes. J. Mol. Evol 28:286-298.
62. VIANEY-LIAUD, M. 1985. Possible evolutionary relationships among Eocene and Lower Oligocence rodents of Asia, Europe and North America. Pages 277-310 in Evolutionary relationships among rodents: A multidisciplinary analysis (W. P. Luckett and J.-L. Hartenberger, eds.). Plenum, New York.
63. WADDELL, P. J., Y. CAO J. HAUF, AND M. HASEGAWA. 1999. Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid invariant sites LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant. Syst. Biol. 48:31-53.
64. WAHLERT, J. H. 1985a. Cranial foramena of rodents. Pages 311-332 in Evolutionary relationships among rodents: A multidisciplinary analysis (W. P. Luckett and J.-L. Hartenberger, eds.). Plenum, New York.
65. WAHLERT, J. H. 1985b. Skull morphology and relationships of geomyoid rodents. Am. Mus. Novit. 2812:1-20.
66. WAHLERT, J. H., S. L. SAWITZKE, AND M. E. HOLDEN. 1993. Cranial anotomy and relationships of dormice (Rodentia, Myoxidae). Am. Mus. Novit. 3061:1-32.
67. WOOD, A. E. 1965. Grades and clades among rodents. Evolution 19:115-130.
68. YANG, Z. 1994. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39:105-111.
69. YANG, Z. 1996a. Among-site rate variation and its impact on phylogenetic analysis. Trends Ecol. Evol. 11:367-372.
70. YANG, Z. 1996b. Maximum likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42:587-596.
71. YANG, Z., N. GOLDMAN, AND A. E. FRIDAY. 1995. Maximum likelihood trees from DNA sequences: A peculiar statistical estimation problem. Syst. Biol. 44:384-399.
72. YODER, A. D., J. A. IRWIN, AND B. A. PAYSEUR. 2001. Failure of the ILD to determine data combinability for slow loris phylogeny. Syst. Biol. 50:408-124.