Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationships equally well [1]

Molecular Biology and Evolution

Volumn 18, Issue 9, 2001, Pages 1823-1827

  Rosenberg, Michael S ^a   Kumar, Sudhir ^a  

^a ARIZONA STATE UNIVERSITY   (United States)

Author keywords

Deep versus shallow branches; Maximum likelihood; Maximum parsimony; Minimum evolution; Neighbor joining; Phylogenetic inference

Indexed keywords

AMINO ACID SUBSTITUTION; COMPUTER SIMULATION; DNA SEQUENCE; LETTER; NONHUMAN; PHYLOGENY; TAXONOMY; TREE;

EID: 0034882680     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a003969     Document Type: Letter

References (21)

1. Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted phylogenetic analysis
2. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
3. Maximum likelihood method of phylogenetic inference from DNA sequence data
4. Inferring complex phylogenies
5. Limitations of the evolutionary parsimony method of phylogenetic analysis
6. Evolution of protein molecules
7. Large-scale phylogenies and measuring the performance of phylogenetic estimators
8. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
9. Efficiency of the neighbor-joining method in reconstructing deep and shallow evolutionary relationships in large phylogenies
10. Reconstruction of phylogenetic trees and estimation of divergence items under non-constant rates of evolution
11. Phylogenetic inference, DNA sequence analysis, and the future of molecular systematics
12. The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small
13. Relative efficiencies of the Fitch-Margoliash, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree
14. Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree
15. Accuracy of neighbor joining for n-taxon trees
16. Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used
17. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
18. Phylogenetic analysis using parsimony and likelihood methods