Uninode coding vs gene tree parsimony for phylogenetic reconstruction using duplicate genes

Molecular Phylogenetics and Evolution

Volumn 23, Issue 3, 2002, Pages 481-498

  Simmons, Mark P ^a   Freudenstein, John V ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA-FETOPROTEINS; ANIMAL; COMPARATIVE STUDY; FRUCTOSE-BISPHOSPHATE ALDOLASE; GENES; HUMAN; MODELS, BIOLOGICAL; MONOPHENOL MONOOXYGENASE; PHYLOGENY; PROLACTIN; PROTEINS; TRYPSINOGEN; VASOPRESSINS; VERTEBRATES; ANIMALS; HUMANS;

VERTEBRATA;

ALPHA FETOPROTEIN; FRUCTOSE BISPHOSPHATE ALDOLASE; MONOPHENOL MONOOXYGENASE; PROLACTIN; PROTEIN; TRYPSINOGEN; VASOPRESSIN DERIVATIVE;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; COMPARATIVE STUDY; GENE; GENETICS; HUMAN; PHYLOGENY; PHYSIOLOGY; VERTEBRATE;

EID: 0036019714     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(02)00033-7     Document Type: Article

References (51)

1. Against consensus
2. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction
3. The early history of modern birds: A comparison of molecular and morphological evidence
4. Sampling properties of DNA sequence data in phylogenetic analysis
5. Duplicate genes and the root of angiosperms, with an example using phytochrome sequences
6. Gene trees and species trees: Molecular systematics as one-character taxonomy
7. Homoplasy connections and disconnections: Genes and species, molecules and morphology
8. The information content of the phylogenetic system
9. The retention index and the rescaled consistency index
10. Parsimony jackknifing outperforms neighbor-joining
11. Confidence limits on phylogenies: An approach using the bootstrap
12. Agnathans and the origin of jawed vertebrates
13. Hidden morphological support for the phylogenetic placement of Pseudoryx nghetinhensis with bovine bovids: A combined analysis of gross anatomical evidence and DNA sequences from five genes
14. Corroboration among data sets in simultaneous analysis: Hidden support for phylogenetic relationships among higher level artiodactyl taxa
15. +-ATPase: Implications for the origin of eukaryotes
16. Fitting the gene lineage into its species lineage: A parsimony strategy illustrated by cladograms constructed from globin sequences
17. Phylogenetic relationships among the section of Clarkia (Onagraceae) inferred from the nucleotide sequences of PgiC
18. Reconstruction of ancient molecular phylogeny
19. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes
20. Evolution of gene families and relationship with organismal evolution: Rapid divergence of tissue-specific genes in the early evolution of chordates
21. A concern for evidence and a phylogenetic hypothesis for relationships among Epicrates (Boidae, Serpentes)
22. Quantitative phyletics and the evolution of Anurans
23. Molecular and morphological supertrees for eutherian (placental) mammals
24. Gene trees in species trees
25. Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparison of sequences
26. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima
27. The parsimony ratchet, a new method for rapid parsimony analysis
28. On simultaneous analysis
29. Component analysis: A valiant failure?
30. Genes, organisms, and areas: The problem of multiple lineages
31. Maps between trees and cladistic analysis of historical associations among genes: Organisms and areas
32. GeneTree: Comparing gene and species phylogenies using reconciled trees
33. Extracting species trees from complex gene trees: Reconciled trees and vertebrate phylogeny
34. From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem
35. Reconciled trees and incongruent gene and species trees
36. Phylogenetic studies of complete mitochondrial DNA molecules place cartilaginous fishes within the tree of bony fishes
37. Molecular studies suggest that cartilaginous fishes have a terminal position in the piscine tree
38. The mitochondrial DNA molecule of the hagfish (Myxine glutinosa) and vertebrate phylogeny
39. Evolution of alcohol dehydrogenase genes in peonies (Paeonia): Phylogenetic relationships of putative nonhybrid species
40. Analysis of taxonomic congruence among morphological, ecological, and biogeographic data sets for the Leptopodomorpha (Hemiptera)
41. Phylogeny reconstruction using duplicate genes
42. Gaps as characters in sequence-based phylogenetic analyses
43. Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses
44. Inferring species trees from gene trees: A phylogenetic analysis of the Elapidae (Serpentes) based on the amino acid sequences of venom proteins
45. How should species phylogenies be inferred from sequence data?
46. Taxonomic congruence in the Leptopodomorpha re-examined
47. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium)