Rate acceleration and long-branch attraction in a conserved gene of cryptic daphniid (Crustacea) species

Molecular Biology and Evolution

Volumn 18, Issue 12, 2001, Pages 2201-2212

  Omilian, Angela R ^a,b   Taylor, Derek J ^a  

^a UNIVERSITY AT BUFFALO   (United States)

^b INDIANA UNIVERSITY   (United States)

Author keywords

Cryptic species; Daphnia; Long branch attraction; Nuclear large subunit; Rate acceleration; rDNA

Indexed keywords

MITOCHONDRIAL DNA; RIBOSOME RNA;

ANIMAL TISSUE; ARTICLE; CELL NUCLEUS; CONTROLLED STUDY; DAPHNIA; DNA SEQUENCE; MAXIMUM LIKELIHOOD METHOD; MOLECULAR EVOLUTION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA SEQUENCE;

DAPHNIA LAEVIS; DAPHNIA OCCIDENTALIS;

EID: 0035207848     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a003767     Document Type: Article

References (61)

1. Cirripede phylogeny using a novel approach: Molecular morphometrics
2. The systematics of North American Daphnia
3. Cryptic sequence simplicity, nucleotide composition bias, and molecular coevolution in the large subunit of ribosomal DNA in plants: Implications for phylogenetic analyses
4. Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters
5. Evolution of the large-subunit ribosomal RNA binding site for protein L23/25
6. The systematics of North American Daphnia (Crustacea: Anomopoda): A molecular phylogenetic approach
7. Sequence of the intergenic space between the 28S and 18S rRNA-encoding genes of the crustacean, Daphnia pulex
8. The origin and evolution of variable-region helices in V4 and V7 of the small-subunit ribosomal RNA of branchiopod crustaceans
9. Best-fit maximum-likelihood models for phylogenetic inference: Empirical tests with known phylogenies
10. The European large subunit ribosomal RNA database
11. The complete nucleotide sequence of the mitochondrial DNA of the agnathan Lampetra fluviatilis: Bearings on the phylogeny of cyclostomes
12. A rapid DNA isolation procedure for small quantities of fresh leaf tissue
13. Cases in which parsimony or compatibility methods will be positively misleading
14. Evolutionary trees from DNA sequences: A maximum likelihood approach
15. An episodic change of rDNA nucleotide substitution rate has occurred during the emergence of the insect order Diptera
16. Success of maximum-likelihood phylogeny inference in the 4-taxon case
17. Likelihood-based tests of topologies in phylogenetics
18. Molecular coevolution among cryptically simple expansion segments of eukaryotic 26S/28S rRNAs
19. Phylogeny and molecular evolution in primates
20. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
21. A framework for the quantitative study of evolutionary trees
22. Experimental phylogenetics: Generation of a known phylogeny
23. Ribosomal DNA: Molecular evolution and phylogenetic inference
24. Signal, noise, and reliability in molecular phylogenetic analyses
25. Performance of phylogenetic methods in simulation
26. Is the Felsenstein zone a fly trap?
27. Systematic bias in phylogenetic analysis: Is the Strepsiptera problem solved?
28. Phylogeny estimation and hypothesis testing using maximum likelihood
29. Monophyly of lampreys and hagfishes supported by nuclear DNA-coded genes
30. The phylogenetic potential of entire 26S rDNA sequences in plants
31. Chromosomes and nuclear-Dna of Crustacea
32. A hierarchical molecular phylogeny within the genus Daphnia
33. Molecular phylogenetics of cupped oysters based on partial 28S rRNA gene sequences
34. A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages
35. 28S and 18S rDNA sequences support the monophyly of lampreys and hagfishes
36. Effects of sequence alignment and structural domains of ribosomal DNA on phylogeny reconstruction for the protozoan family Sarcocystidae
37. Simplicity-correlated size growth of the nuclear 28S ribosomal RNA D3 expansion segment in the crustacean order Isopoda
38. A phylogenetic analysis of the Conchostraca and Cladocera (Crustacea Branchiopoda, Diplostraca)
39. MODELTEST: Testing the model of DNA substitution
40. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic frees
41. The general stochastic model of nucleotide substitution
42. Parametric phylogenetics?
43. Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants
44. Multiple comparisons of log-likelihoods with applications to phylogenetic inference
45. Invariable sites models and their use in phylogeny reconstruction
46. Long-branch attraction and the rDNA model of early eukaryotic evolution
47. PAUP*: Phylogenetic analysis using parsimony (*and other methods). Version 4.Ob8
48. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
49. Cryptic sequence simplicity in DNA is a major source of genetic variation
50. Phylogenetic evidence for a single long-lived clade of crustacean cyclic parthenogens and its implications for the evolution of sex
51. Biogeography of a widespread freshwater crustacean: Pseudocongruence and cryptic endemism in the North American Daphnia laevis complex
52. Phylogenetics and evolution of the Daphnia longispina group (Crustacea) based on 12S rDNA sequence and allozyme variation
53. The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
54. Clustal-W - Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
55. rRNA processing: Removal of only nineteen bases at the gap between 28S alpha and 38S beta rRNA in Sciara coprophila
56. War of the iguanas: Conflicting molecular and morphological phylogenies and long-branch attraction in Iguanid lizards
57. Phylogenetic position of the Strepsiptera: Review of molecular and morphological evidence