Long-branch attraction phenomenon and the impact of among-site rate variation on rodent phylogeny

Gene

Volumn 259, Issue 1-2, 2000, Pages 177-187

  Reyes, Aurelio ^a   Pesole, Graziano ^b   Saccone, Cecilia ^a,c  

^a CNR   (Italy)

^b UNIVERSITY OF MILAN   (Italy)

^c UNIVERSITY OF BARI   (Italy)

Author keywords

Gamma distribution; Mitochondrial genome; Rodent monophyly; Rodent paraphyly

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; DNA SEQUENCE; GENETIC VARIABILITY; GENOME; GUINEA PIG; MITOCHONDRION; MOLECULAR EVOLUTION; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RAT; RIBOSOME; RODENT; SEQUENCE ANALYSIS; SQUIRREL;

ANIMALS; DATABASES, FACTUAL; DNA, MITOCHONDRIAL; HUMANS; PHYLOGENY; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 16S; RODENTIA; VARIATION (GENETICS);

CAVIA PORCELLUS; MAMMALIA; MURIDAE; RODENTIA; SCIURIDAE; SUS SCROFA;

EID: 0034707205     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(00)00438-8     Document Type: Article

References (62)

1. MOLPHY version 2.3: Programs for molecular phylogenetics based on maximum likelihood
2. Evolution of eutherian cytochrome c oxidase subunit II: Heterogeneous rates of protein evolution and altered interaction with cytochrome c
3. Beitrage zur nahern Kenntniss der Saugethiere Russlands
4. Phylogeny of insectivores mammals
5. Phylogenetic position of guinea pigs revisited
6. Molecular systematics of Hystricognath rodents: The contribution of Sciurognath mitochondrial 12S rRNA sequences
7. The guinea-pig is not a rodent
8. Cases in which parsimony or compatibility methods will be positively misleading
9. A method for estimating the number of invariant amino acid positions in a gene using cytochrome c as a model case
10. The effectiveness of mitochondrial rRNA gene sequences for the reconstrucion of the phylogeny of an insect order (Orthoptera)
11. Success of maximum likelihood phylogeny inference in the four-taxon case
12. Lineage-specific evolutionary rate in mammalian mtDNA
13. Is it better to add taxa or characters to a difficult phylogenetic problem?
14. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites
15. The order Rodentia: Major questions on their evolutionary origin, relationships and suprefamilial systematics
16. Les debuts de la radiation adaptive des Rodentia (Mammalia)
17. Description de la radiation des Rodentia (Mammalia) du Palèocene superieur au Miocene, incidences phylogenetiques
18. A framework for the quantitative study of evolutionary trees
19. Inferring complex philogenies
20. Taxonomic sampling, phylogenetic accuracy and investigator bias
21. Mammalian mitochondrial DNA evolution: A comparison of the cytochrome b and cytochrome c oxidase II genes
22. Molecular evolution of the nuclear von Willebrand factor gene in mammals and the phylogeny of rodents
23. Performance of phylogenetic methods in simulation
24. Is the Felsenstein zone a fly trap?
25. Rodent phylogeny: New data and old problems
26. General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing number of taxa
27. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA seqeunce data, and the branching order in Hominoidea
28. Species sampling has a major impact on phylogenetic inference
29. The molecular taxonomy and evolution of the guinea pig
30. Monophyly or polyphyly of the order Rodentia: Possible conflict between morphological and molecular interpretations
31. Relative apparent synapomorphy analysis (RASA). I. The statistical measurement of phylogenetic signal
32. Definition and relationships of Lipotyphla
33. Molecular phylogeny of the springhare, Pedetes capensis, based on mitochondrial DNA sequences
34. Unusually high evolutionary rate of the elongation factor 1 α genes from the Ciliophora and its impact on the phylogeny of eukaryotes
35. The phylogenetic position of the Talpidae within Euteria based on analysis of complete mitochondrial sequences
36. Molecular systematics of hystricognath rodents: Evidence from the mitochondrial 12S rRNA gene
37. Higher-level systematics of rodents (Mammalia, Rodentia): Evidence from the mitochondrial 12S rRNA gene
38. Rodent monophyly: Pitfalls of molecular phylogenies
39. How good are deep phylogenetic trees?
40. Sensitivity of phylogeny estimation to taxonomic sampling
41. Are big trees indeed easy?
42. Taxon sampling and the accuracy of large phylogenies
43. Complete mitochondrial DNA sequence of the fat dormouse, Glis glis: Further evidence of rodent paraphyly
44. Where do rodents fit? Evidence from the complete mitochondrial genome of Sciurus vulgaris
45. Molecular phylogeny of rodents, with special emphasis on murids: Evidence from nuclear gene LCAT
46. A simple method for estimating and testing minimum evolution trees
47. Influence of base composition on quantitative estimates of gene evolution
48. Endemic African mammals shake the phylogenetic tree
49. Molecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals
50. Molecular systematics and phylogeography of the Peromyscus aztecus species group (Rodentia: Muridae) inferred using parsimony and likelihood
51. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics
52. The effect of taxon sampling on estimating rate heterogeneity parameters of maximum-likelihood models
53. Correct and incorrect vertebrate phylogenies obtained by the entire mitochondrial DNA sequences
54. The phylogenetic relationships of the suborder Aconthuroidei (Teleostei: Perciformes) based on molecular and morphological evidence
55. Ueber das System der Nagetiere: Eine phylogenetische Studie
56. Fitting discrete probability distributions to evilutionary events
57. Estimating the pattern of nucleotide substitution
58. Among-site rate variation and its impact on phylogenetic analyses