Bayesian and maximum likelihood analyses of rotifer-acanthocephalan relationships

Hydrobiologia

Volumn 546, Issue 1, 2005, Pages 47-54

  Mark Welch, David B ^a  

^a MARINE BIOLOGICAL LABORATORY   (United States)

Author keywords

18S; Eurotatoria; Gnathifera; Phylogenetics; Syndermata

Indexed keywords

CYTOLOGY; DNA SEQUENCES; GENETIC ENGINEERING; MATHEMATICAL MODELS; MAXIMUM LIKELIHOOD ESTIMATION; NUCLEIC ACIDS; PHYSIOLOGY; PROTEINS; STATISTICAL METHODS;

18S; EUROTATORIA; GNATHIFERA; PHYLOGENETICS; SYNDERMATA;

MARINE BIOLOGY;

BAYESIAN ANALYSIS; EVOLUTION; MAXIMUM LIKELIHOOD ANALYSIS; PHYLOGENY;

ACANTHOCEPHALA (WORMS); ACANTHOCEPHALUS; BDELLOIDEA (ROTIFERA); MONOGONONTA; ROTIFERA; SEISONIDEA;

EID: 24144461149     PISSN: 00188158     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10750-005-4100-y     Document Type: Conference Paper

References (46)

1. E. Abouheif R. Zardoya A. Meyer 1998 Limitations of metazoan 18S rRNA sequence data: implications for reconstructing a phylogeny of the animal kingdom and inferring the reality of the Cambrian explosion Journal of Molecular Evolution 47 394 405
2. M. E. Alfaro S. Zoller F. Lutzoni 2003 Bayes or Bootstrap? A simulation study comparing the performance of Bayesian Markov Chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence Molecular Biology and Evolution 20 255 266
3. W. H. Ahlrichs 1997 Epidermal ultrastructure of Seison nebaliae and Seison annulatus, and a comparison of epidermal structures within the Gnathifera Zoomorphology 117 41 48
4. M. P. Cummings S. P. Otto J. Wakeley 1995 Sampling properties of DNA sequence data in phylogenetic analysis Molecular Biology and Evolution 12 814 822
5. M. P. Cummings S. A. Handley D. S. Myers D. L. Reed A. Rokas K. Winka 2003 Comparing bootstrap and posterior probability values in the four-taxon case Systematic Biology 52 477 487
6. M. P. Cummings S. P. Otto J. Wakeley 1999 Genes and other samples of DNA sequence data for phylogenetic inference Biological Bulletin 196 532 540
7. C. J. Douady F. Delsuc Y. Baoucher W. F. Doolittle E. J. P. Douzery 2003 Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability Molecular Biology and Evolution 20 248 254
8. M. García-Varela G. Pérez-Ponce de León P. de la Torre M. P. Cummings S. S. S. Sarma J. P. Laclette 2000 Phylogenetic relationships of Acanthocephala based on analysis of 18S ribosomal RNA gene sequences Journal of Molecular Evolution 50 532 554
9. J. R. Garey T. J. Near M. R. Nonnemacher S. A. Nadler 1996 Molecular evidence for Acanthocephala as a subtaxon of Rotifera Journal of Molecular Evolution 43 287 292
10. J. R. Garey A. Schmidt-Rhaesa T. J. Near S. A. Nadler 1998 The evolutionary relationships of rotifers and acanthocephalans Hydrobiologia 387/388 83 91
11. J. J. Gilbert 1983 Rotifera K. G. Adiyodi R. G. Adiyodi Reproductive Biology of Invertebrates Vol. 1. John Wiley & Sons Chichester, NY 181 209
12. A. Graybeal 1998 Is it better to add taxa or characters to a difficult phylogenetic problem? Systematic Biology 47 9 17
13. J. M. Hancock A. P. Vogler 2000 How slippage-derived sequences are incorporated into rRNA variable-region secondary structure: implications for phylogeny reconstruction Molecular Phylogenetics and Evolution 14 366 374
14. H. Herlyn O. Piskurek J. Schmitz U. Ehlers H. Zischler 2003 The syndermatan phylogeny and the evolution of acanthocephalan endoparasitism as inferred from 18S rDNA sequences Molecular Phylogenetics and Evolution 26 155 164
15. D. M. Hillis 1996 Inferring complex phylogenies Nature 388 130
16. D. M. Hillis 1998 Taxonomic sampling, phylogenetic accuracy, and investigator bias Systematic Biology 47 3 8
17. D. M. Hillis J. J. Hill 1993 An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis Systematic Biology 42 182 192
18. J. P. Huelsenbeck F. Ronquist 2001 MRBAYES: Bayesian inference of phylogenetic trees Bioinformatics 17 754 755
19. H. Kishino M Hasegawa 1989 Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea Journal of Molecular Evolution 29 170 179
20. G. Lecointre H. Philippe H. L. V. Lê H. Le Guyader 1993 Species sampling has a major impact on phylogenetic inference Molecular Phylogenetics and Evolution 2 205 224
21. L. E. Maley C. R Marshall 1998 The coming of age of molecular systematics Science 279 505 506
22. D. B. Mark Welch 2000 Evidence from a protein-coding gene that acanthocephalans are rotifers Invertebrate Biology 111 17 23
23. D. B. Mark Welch 2001 Early contributions of molecular phylogenetics to understanding the evolution of Rotifera Hydrobiologia 446/447 315 322
24. D. B. Mark Welch M. Meselson 2000 Evidence for the evolution of bdelloid rotifers without sexual reproduction or genetic exchange Science 288 2111 2115
25. D. B. Mark Welch M. Meselson 2001 Rates of nucleotide evolution in sexual and anciently asexual rotifers Proceedings of the National Academy of Sciences USA 98 6720 6724
26. T. Near 2002 Acanthocephalan phylogeny and the evolution of parasitism Integrative and Comparative Biology 42 668 677
27. A. R. Omilian D. J. Taylor 2001 Rate acceleration and long-branch attraction in a conserved gene of cryptic Daphniid (Crustacea) species Molecular Biology and Evolution 18 2201 2212
28. S. P. Otto M. P. Cummings J. Wakeley 1996 Inferring phylogenies from DNA sequence data: the effects of sampling P. H. Harvey A. J. Leigh Brown J. Maynard Smith S. Nee New Uses for New Phylogenies Oxford University Press Oxford
29. H. Philippe A. Germot 2000 Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of sequence evolution Molecular Biology and Evolution 17 830 834
30. S. Poe 1998 Sensitivity of phylogeny estimation to taxonomic sampling Systematic Biology 47 18 31
31. S. Poe D. L. Swofford 1999 Taxon sampling revisited Nature 398 299 300
32. D. Posada K. A. Crandall 1998 MODELTEST: testing the model of DNA substitution Bioinformatics 14 917 818
33. C. Ricci G. Melone C. Sotgia 1993 Old and new data on Seisonidea (Rotifera) Hydrobiologia 255/256 495 511
34. F. Rodríguez J. F. Oliver A. Marín J. R. Medina 1990 The general stochastic model of nucleotide substitution Journal of Theoretical Biology 142 485 501
35. H. Segers 2002 The nomenclature of the Rotifera: annotated checklist of valid family- and genus-group names Journal of Natural History 36 631 640
36. H. Segers R. J. Shiel 2005 Tale of a sleeping beauty: a new and easily cultured model organism for experimental studies on bdelloid rotifers Hydrobiologia 546 141 145
37. H. Shimodaira M. Hasegawa 1999 Multiple comparisons of log-likelihoods with applications to phylogenetic inference Molecular Biology and Evolution 16 1114 1116
38. J. Sullivan D. L Swofford 1997 Are guinea pigs rodents? The importance of adequate models in molecular evolution Journal of Mammalian Evolution 2 77 86
39. Y. Suzuki G. V. Glazko M. Nei 2002 Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics Proceedings of the National Academy of Science USA 99 16138 16143
40. Swofford, D. L., 2002. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, MA
41. K. Tamura M. Nei 1993 Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees Molecular Biology and Evolution 10 512 526
42. J. D. Thompson D. G. Higgins 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 Research 22 4673 4680
43. R. L. Wallace 1999 Phylum Rotifera E. Knobil J. D. Neill Encyclopedia of Reproduction Vol. 4. Academic Press San Diego, CA 118 129
44. R. L. Wallace 2002 Rotifers: exquisite metazoans Integrative and Comparative Biology 42 660 667
45. T. P. Wilcox D. J. Zwickl T. A. Heath D. M. Hillis 2002 Phylogenetic relationships of dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support Molecular Phylogenetics Evolution 25 361 371
46. Z. Yang 1997 PAML: a program package for phylogenetic analysis by maximum likelihood Computer Applications in the Biosciences 15 555 556