War of the iguanas: Conflicting molecular and morphological phylogenies and long-branch attraction in iguanid lizards

Systematic Biology

Volumn 49, Issue 1, 2000, Pages 143-159

  Wiens, John J ^a   Hollingsworth, Bradford D ^b,c  

^a SECTION OF VERTEBRATE PALEONTOLOGY   (United States)

^b LOMA LINDA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c SAN DIEGO NATURAL HISTORY MUSEUM   (United States)

Author keywords

Data set incongruence; Iguanidae; Likelihood; Long branch attraction, parsimony

Indexed keywords

AMBLYRHYNCHUS; CONOLOPHUS; CYCLURA; IGUANA; IGUANIA; IGUANIDAE; SAUROMALUS; SQUAMATA;

DNA;

ANIMAL; ARTICLE; CLASSIFICATION; GENETICS; LIZARD; NUCLEOTIDE SEQUENCE; PHYLOGENY;

ANIMALS; BASE SEQUENCE; DNA; IGUANAS; LIZARDS; PHYLOGENY;

EID: 0034350374     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150050207447     Document Type: Article

References (73)

1. BAKER, R. H., X. Yu, AND R. DESALLE. 1998. Assessing the relative contribution of molecular and morphological characters in simultaneous analysis trees. Mol. Phylogenet. Evol. 9:427-436.
2. 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. 42:384-4197.
3. BURGHARDT, G. M., AND A. S. RAND (eds.). 1982. Iguanas of the world: Their behavior, ecology, and conservation. Noyes Publications, Park Ridge, New Jersey.
4. CHIPPINDALE, P. T., AND J. J. WIENS. 1994. Weighting, partitioning, and combining characters in phylogenetic analysis. Syst. Biol. 43:278-287.
5. CUNNINGHAM, C. W. 1997. Can three incongruence tests predict when data should be combined? Mol. Biol. Evol. 14:733-740.
6. DE QUEIROZ, A. 1993. For consensus (sometimes). Syst. Biol. 42:368-372.
7. DE QUEIROZ, A., M. J. DONOGHUE, AND J. KIM. 1995. Separate versus combined analysis of phylogenetic evidence. Annu. Rev. Ecol. Syst. 26:657-681.
8. DE QUEIROZ, K. 1987. Phylogenetic systematics of iguanine lizards. A comparative osteological study. Univ. Calif. Publ. Zool. 118:1-203.
9. DONOGHUE, M. J., AND M. J. SANDERSON. 1992. The suitability of molecular and morphological evidence in reconstructing plant phylogeny. Pages 340-368 in Molecular systematics in plants (P. S. Soltis, D. E. Soltis, and J. J. Doyle, eds.). Chapman and Hall, New York.
10. EMERSON, S. B., AND P. A. HASTINGS. 1998. Morphological correlations in evolution: Consequences for phylogenetic analysis. Q. Rev. Biol. 73:141-162.
11. ETHERIDGE, R., AND K. DE QUEIROZ. 1988. A phylogeny of Iguanidae. Pages 283-368 in Phylogenetic relationships of the lizard families: Essays commemorating Charles L. Camp (R. Estes and G. Pregill, eds.). Stanford University Press, Stanford, California.
12. FARRIS, J. S., M. KALLERSJO, A. G. KLUGE, AND C. BULT. 1994. Testing significance of incongruence. Cladistics 10:315-319.
13. FELSENSTEIN, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
14. FELSENSTEIN, J. 1981. Evolutionary trees from gene frequencies and quantitative characters: Finding maximum likelihood estimates. Evolution 35:1229-1242.
15. FELSENSTEIN, J. 1985a. Confidence limits on phytogenies: An approach using the bootstrap. Evolution 39:783-791.
16. FELSENSTEIN, J. 1985b. Confidence limits on phytogenies with a molecular clock. Syst. Zool. 34:152-161.
17. FROST, D. R., AND R. ETHERIDGE. 1989. A phylogenetic analysis and taxonomy of iguanian lizards (Reptilia: Squamata). Misc. Publ. Mus. Nat. Hist. Univ. Kansas 81:1-65.
18. GRAYBEAL, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47:9-17.
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. HASEGAWA, M., H. KISHINO, AND T. YANO. 1985. Dating the human-ape split by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
21. HEDGES, S. B., AND MAXSON, L. R. 1996. Re: Molecules and morphology in amniote phylogeny. Mol. Phylogenet. Evol. 6:312-314.
22. HILLIS, D. M. 1987. Molecular versus morphological approaches to systematics. Annu. Rev. Ecol. Syst. 18:23-42.
23. HILLIS, D. M. 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47: 3-8.
24. HILLIS, D. M., AND J. J. BULL. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:182-192.
25. HOLLINGSWORTH, B. D. 1998. The systematics of chuckwallas (Sauromalus) with a phylogenetic analysis of other iguanid lizards. Herpetol. Monogr. 12:38-191.
26. HUELSENBECK, J. P. 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44:17-48.
27. HUELSENBECK, J. P. 1997. Is the Felsenstein Zone a fly trap? Syst. Biol. 46:69-74.
28. HUELSENBECK, J. P. 1998. Systematic bias in phylogenetic analysis: Is the Strepsiptera problem solved? Syst. Biol. 47:519-537.
29. HUELSENBECK, J. P., AND J. J. BULL. 1996. A likelihood ratio test to detect conflicting phylogenetic signal. Syst. Biol. 45:92-98.
30. HUELSENBECK, J. P., J. J. BULL, AND C. W. CUNNINGHAM. 1996a. Combining data in phylogenetic analysis. Trends Ecol. Evol. 11:152-158.
31. HUELSENBECK, J. P., AND K. A. CRANDALL. 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Rev. Ecol. Syst. 28:437-466.
32. HUELSENBECK, J. P., D. M. HILLIS, AND R. JONES. 1996b. Parametric bootstrapping in molecular phylogenetics: Application and performance. Pages 19-45 in Molecular zoology: Advances, strategies, and protocols (J. D. Ferraris and S. R. Palumbi, eds.). Wiley-Liss, New York.
33. JUKES, T. H., AND C. R. CANTOR. 1969. Evolution of protein molecules. Pages 21-132 in Mammalian protein metabolism (H. N. Munro, ed.). Academic Press, New York.
34. KIMURA, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
35. KJER, K. M. 1995. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: An example of alignment and data presentation from frogs. Mol. Phylogenet. Evol. 4:314-330.
36. KLUGE, A. G., AND A. J. WOLF. 1993. Cladistics: What's in a word? Cladistics 9:183-199.
37. LARSON, A. 1994. The comparison of molecular and morphological data in phylogenetic systematics. Pages 371-390 in Molecular ecology and evolution: Approaches and applications (B. Schierwater, B. Streit, G. P. Wagner, and R. DeSalle, eds.). Birkauser Verlag, Basel, Switzerland.
38. MADDISON, W. P., AND D. R. MADDISON. 1992. MacClade Ver. 3.O. Analysis of phylogeny and character evolution. Sinauer, Sunderland.
39. MEYER, A. 1994. Shortcomings of the cytochrome b gene as a molecular marker. Trends Ecol. Evol. 9: 278-280.
40. MICKEVICH, M. F., AND J. S. FARRIS. 1981. The implications of congruence in Menidia. Syst. Zool. 30:351-370.
41. MIYAMOTO, M. 1996. A congruence study of the molecular and morphological data for eutherian mammals. Mol. Phylogenet. Evol. 6:373-390.
42. NORELL, M. A., AND K. DE QUEIROZ. 1991. The earliest iguanine lizard (Reptilia; Squamata) and its bearing on iguanine phylogeny. Am. Mus. Novit. 2997: 1-16.
43. NORMARK, B. B., AND A. A. LANTERI. 1998. Incongruence between morphology and mitochondrial-DNA characters suggests hybrid origins of parthenogenetic weevil lineages (genus Aramigus). Syst. Biol. 47: 475-494.
44. OMLAND, K. E. 1997. Correlated rates of molecular and morphological evolution. Evolution 51:1381-1393.
45. PATTERSON, C., D. M. WILLIAMS, AND C. J. HUMPHRIES. 1993. Congruence between molecular and morphological phylogenies. Annu. Rev. Ecol. Syst. 24:153-188.
46. PETREN, K., AND T. J. CASE. 1997. A phylogenetic analysis of body size evolution and biogeography in chuckwallas (Sauromalus) and other iguanines. Evolution 51:206-219.
47. POE, S. 1996. Data set incongruence and the phylogeny of crocodilians. Syst. Biol. 45:393-414.
48. RASSMANN, K. 1997. Evolutionary age of the Galápagos iguanas predates the age of the present Galapagos islands. Mol. Phylogenet. Evol. 7:158-172.
49. RODRIGO, A. G., M. KELLY-BORGES, P. R. BERGQUIST, AND P. L. BERGQUIST. 1993. A randomization test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree. N.Z. J. Bot. 31:257-268.
50. ROHLF, F. J., AND R. R. SOKAL. 1981. Statistical tables, 2nd edition. W. H. Freeman, San Francisco, California.
51. SIDDALL, M. E. 1998. Success of parsimony in the four-taxon case: Long branch repulsion by likelihood in the Farris Zone. Cladistics 14:209-220.
52. SITES, J. W., JR., S. K. DAVIS, T. GUERRA, J. B. IVERSON, AND H. L. SNELL. 1996. Character congruence and phylogenetic signal in molecular and morphological data sets: A case study in the living iguanas (Squamata: Iguanidae). Mol. Biol. Evol. 13:1087-1105.
53. SULLIVAN, J., J. A. MARKERT, AND C. W. KILPATRICK. 1997. Phylogeography and molecular systematics of the Peromyscus aztecus species group (Rodentia: Muridae) inferred using parsimony and likelihood. Syst. Biol. 46:426-440.
54. 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.
55. SWOFFORD, D. L. 1991. When are phylogeny estimates from molecular and morphological data incongruent? Pages 295-333 in Phylogenetic analysis of DNA sequences (M. M. Miyamoto and J. Cracraft, eds.). Oxford Univ. Press, New York.
56. SWOFFORD, D. L. 1998. PAUP*: Phylogenetic analysis using parsimony*. Ver. 4.0.0d63. Sinauer, Sunderland, Massachusetts.
57. SWOFFORD, D. L., G. J. OLSEN, P. J. WADDELL, AND D. M. HILLIS. 1996. Phylogeny reconstruction. Pages 407-514 in Molecular systematics, 2nd edition (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer, Sunderland, Massachusetts.
58. TEMPLETON, A. R. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and apes. Evolution 37:221-244.
59. THOMPSON, J. D., D. G. HIGGINS, AND T. J. GIBSON. 1994. CLUSTAL W: 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. TITUS, T. A., AND D. R. FROST. 1996. Molecular homology assessment and phylogeny in the lizard family Opluridae (Squamata: Iguania). Mol. Phylogenet. Evol. 5:49-62.
61. 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.
62. WIENS, J. J. 1995. Polymorphic characters in phylogenetic systematics. Syst. Biol. 44:482-500.
63. WIENS, J. J. 1998a. Testing phylogenetic methods with tree-congruence: Phylogenetic analysis of polymorphic morphological characters in phrynosomatid lizards. Syst. Biol. 47:427-444.
64. WIENS, J. J. 1998b. The accuracy of methods for coding and sampling higher-level taxa for phylogenetic analysis: A simulation study. Syst. Biol. 47:397-413.
65. WIENS, J. J. 1998c. Does adding characters with missing data increase or decrease phylogenetic accuracy? Syst. Biol. 47:625-640.
66. WIENS, J. J. 1998d. Combining data sets with different phylogenetic histories. Syst. Biol. 47:568-581.
67. WIENS, J. J., AND T. W. REEDER. 1995. Combining data sets with different numbers of taxa for phylogenetic analysis. Syst. Biol. 44:548-558.
68. WIENS, J. J., AND T. W. REEDER. 1997. Phylogeny of the spiny lizards (Sceloporus) based on molecular and morphological evidence. Herpetol. Monogr. 11:1-101.
69. WIENS, J. J., AND M. R. SERVEDIO. 1997. Accuracy of phylogenetic analysis including and excluding polymorphic characters. Syst. Biol. 46:332-345.
70. WIENS, J. J., AND M. R. SERVEDIO. 1998. Phylogenetic analysis and intraspecific variation: Performance of parsimony, likelihood, and distance methods. Syst. Biol. 47:228-253.
71. YANG, Z. 1994. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39:306-314.
72. YANG, Z. 1996. Phylogenetic analysis using parsimony and likelihood methods. J. Mol. Evol. 42:294-307.
73. YANG, Z., N. GOLDMAN, AND A. FRIDAY. 1995. Maximum likelihood trees from DNA sequences: A peculiar statistical estimation problem. Syst. Biol. 44: 384-399.