Shared nucleotide composition biases among species and their impact on phylogenetic reconstructions of the Drosophilidae

Molecular Biology and Evolution

Volumn 18, Issue 8, 2001, Pages 1464-1473

  Tarrio R ^a   Rodriguez Trelles F ^a   Ayala, F J ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Drosophilidae; Heterogeneous GC content; Maximum likelihood phylogeny; Molecular phylogeny; Nonhomogeneous phylogeny models; Unequal base composition

Indexed keywords

NUCLEOTIDE;

ARTICLE; DNA SEQUENCE; DROSOPHILA; GENETIC ANALYSIS; GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ANALYSIS; SPECIES DIFFERENCE;

EID: 0034907489     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a003932     Document Type: Article

References (56)

1. What can and what cannot be inferred from pairwise sequence comparisons?
2. Bestfit maximum-likelihood models for phylogenetic inference: Empirical tests with known phylogenies
3. The phylogenetic relationships of the flies in the family Drosophilidae deduced from mtDNA sequences
4. Confidence limits on phylogenies: An approach using the bootstrap
5. Phylogenies from molecular sequences: Inference and reliability
6. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions
7. Inferring phylogenies from DNA sequences of unequal base compositions
8. Inferring the pattern and process: Maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis
9. Isochore evolution in mammals: A human-like ancestral structure
10. A nonhyperthermophilic common ancestor to extant life forms
11. Likelihood-based tests of topologies in phylogenetics
12. Statistical tests of gamma distributed rate heterogeneity in models of sequence evolution in phylogenetics
13. A phylogenetic revised classification of genera in the Drosophilidae (Diptera)
14. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis
15. The performance of phylogenetic methods in simulation
16. Phylogeny estimation and hypothesis testing using maximum likelihood
17. Evolution of protein molecules
18. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
19. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from the DNA sequence data, and the branching order in Hominoidea
20. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
21. Phylogeny of Drosophila and related genera: Conflict between molecular and anatomical analyses
22. Phylogeny of Drosophila and related genera inferred from the nucleotide sequence of the Cu,Zn Sod gene
23. Recovering evolutionary trees under a more realistic model of sequence evolution
24. Molecular phylogeny of Drosophila based on ribosomal RNA sequences
25. Drosophila molecular phylogenies and their uses
26. Character congruence of multiple data partitions and the origin of the Hawaiian Drosophilidae
27. Switch in codon bias and increased rates of amino acid substitution in the Drosophila saltans species group
28. Fluctuating mutation bias and the evolution of the base composition in Drosophila
29. Disparate evolution of paralogous introns in the Xdh gene of Drosophila
30. Evidence for a high ancestral GC content in Drosophila
31. Molecular phylogeny and divergence times of Drosophilid species
32. Tests of the applicability of several substitution models for DNA sequence data
33. Invariable sites models and their use in phylogenetic reconstruction
34. Confidence in evolutionary trees from biological sequence data
35. Reconstructing trees when sequence sites evolve at variable rates
36. Phylogenetic inference
37. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C content biases
38. New Drosophila introns originate by duplication
39. Tree rooting with outgroups when they differ in their nucleotide composition from the ingroup: The Drosophila saltans and willistoni groups, a case study
40. On the evolution of Dopa decarboxylase (Ddc) and Drosophila systematics
41. Some probabilistic and statistical problems on the analysis of DNA sequences
42. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice
43. The phylogeny ecology and geography of Drosophila
44. Performance of the relative-rate test under nonstationary models of nucleotide substitution
45. The Drosophilidae: A taxonomic overview
46. Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics
47. Hierarchical analysis of variation in the mitochondrial 16S rRNA gene among Hymenoptera
48. The evolution of duplicate glyceraldehyde-3-phosphate dehydrogenase genes in Drosophila
49. Estimating the pattern of nucleotide substitution
50. The among-site rate variation and its impact on phylogenetic analyses
51. Comparison of models for nucleotide substitution used in maximum likelihood phylogenetic estimation
52. On the use of nucleic acid sequences to infer branchings in the tree of life