Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Volumn 304, Issue 1, 2005, Pages 64-74

  Gadagkar, Sudhindra R ^a   Rosenberg, Michael S ^b,c   Kumar, Sudhir ^b,c  

^a UNIVERSITY OF DAYTON   (United States)

^b ARIZONA STATE UNIVERSITY   (United States)

^c ARIZONA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONCATENATED DNA;

ANIMAL; ARTICLE; COMPUTER SIMULATION; GENE; GENETICS; MAMMAL; PHYLOGENY;

ANIMALS; COMPUTER SIMULATION; DNA, CONCATENATED; GENES; MAMMALS; PHYLOGENY;

EID: 14844313275     PISSN: 15525007     EISSN: None     Source Type: Journal    
DOI: 10.1002/jez.b.21026     Document Type: Article

References (41)

1. Amrine-Madsen H, Koepfli KP, Wayne RK, Springer MS. 2003. A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships. Mol Phylogenet Evol 28:225-240.
2. Baldauf SL. 1999. A search for the origins of animals and fungi: comparing and combining molecular data. Am Nat 154:S178-S188.
3. Barrett M, Donoghue MJ, Sober E. 1991. Against consensus. Syst Zool 40:486-493.
4. Bull JJ, Huelsenbeck JP, Cunningham CW, Swofford DL, Waddell PJ. 1993. Partitioning and combining data in phylogenetic analysis. Syst Biol 42:384-397.
5. de Queiroz A. 1993. For consensus (sometimes). Syst Biol 42:368-372.
6. de Queiroz A, Donoghue MJ, Kim J. 1995. Separate versus combined analysis of phylogenetic evidence. Annu Rev Ecol Syst 26:657-681.
7. Delsuc F, Stanhope MJ, Douzery EJP. 2003. Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genes. Mol Phylogenet Evol 28:261-275.
8. Doyle JA. 1992. Gene trees and species trees: molecular systematics as one-character taxonomy. Syst Botany 17:144-163.
9. Doyle JA, Donoghue MJ, Zimmer EA. 1994. Integration of morphological and rRNA data on the origin of angiosperms. Ann Missouri Bot Gard 81:419-450.
10. Duret L, Mouchiroud D, Gouy M. 1994. HOVERGEN: a database of homologous vertebrate genes. Nucleic Acids Res 22:2360-2365.
11. Eizirik E, Murphy WJ, O'Brien SJ. 2001. Molecular dating and biogeography of the early placental mammal radiation. J Hered 92:212-219.
12. Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401-410.
13. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
14. Hedges SB, Blair JE, Venturi ML, Shoe JL. 2004. A molecular time scale of eukaryote evolution and the rise of complex multicellular life. BMC Evol Biol 4:2.
15. Hillis DM. 1987. Molecular versus morphological approaches to systematics. Annu Rev Ecol Syst 18:23-42.
16. Hoofer SR, Reeder SA, Hansen EW, Van den Bussche RA. 2003. Molecular phylogenetics and taxonomic review of noctilionoid and vespertilionoid bats (Chiroptera: Yangochiroptera). J Mammal 84:809-821.
17. Huelsenbeck JP, Bull JJ, Cunningham CW. 1996. Combining data in phylogenetic analysis. Trends Ecol Evol 11:152-158.
18. Huelsenbeck JP, Swofford DL, Cunningham CW, Bull JJ, Waddell PJ. 1994. Is character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis? Syst Biol 43:288-291.
19. Jukes TH, Cantor CR. 1969. Evolution of protein molecules. In: Munro HN, editor. Mammalian protein metabolism. New York: Academic Press. p 21-132.
20. Kumar S, Gadagkar SR. 2000. Efficiency of the neighbor-joining method in reconstructing deep and shallow evolutionary relationships in large phylogenies. J Mol Evol 51(6):544-553.
21. Miyamoto MM, Fitch WM. 1995. Testing species phylogenies and phylogenetic methods with congruence. Syst Biol 44:64-76.
22. Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryderk OA, O'Brien SJ. 2001. Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618.
23. Nei M, Kumar S. 2000. Molecular evolution and phylogenetics. New York: Oxford University Press.
24. Nei M, Xu P, Glazko G. 2001. Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms. Proc Natl Acad Sci U S A 98:2497-2502.
25. Olmstead RG, Sweere JA. 1994. Combining data in phylogenetic systematics - an empirical approach using 3 molecular data sets in the Solanaceae. Syst Biol 43:467-481.
26. Penny D, Hendy MD. 1985. The use of tree comparison metrics. Syst Zool 34:75-82.
27. Phillips MJ, Delsuc F, Penny D. 2004. Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol 21:1455-1458.
28. Robinson DF, Foulds LR. 1981. Comparison of phylogenetic trees. Math Biosci 53(1-2):131-147.
29. Rodrigo AG, Kellyborges M, Bergquist PR, Bergquist PL. 1993. A randomization test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree. New Zealand J Bot 31:257-268.
30. Rokas A, Williams BL, King N, Carroll SB. 2003. Genomescale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804.
31. Rosenberg MS, Kumar S. 2001. Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationships equally well. Mol Biol Evol 18:1823-1827.
32. Rosenberg MS, Kumar S. 2003. Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Mol Biol Evol 20:610-621.
33. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425.
34. Shevchuk NA, Allard MW. 2001. Sources of incongruence among mammalian mitochondrial sequences: COII, COIII, and ND6 genes are main contributors. Mol Phylogenet Evol 21:43-54.
35. Suchard MA, Kitchen CMR, Sinsheimer JS, Weiss RE. 2003. Hierarchical phylogenetic models for analyzing multipartite sequence data. Syst Biol 52:649-664.
36. Swofford DL. 2001. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4.0b10. Sunderland, MA: Sinauer Associates.
37. Tamura K, Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512-526.
38. Tamura K, Nei M, Kumar S. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 101(30):11030-11035.
39. Teeling EC, Madsen O, Murphy WJ, Springer MS, O'Brien J. 2003. Nuclear gene sequences confirm an ancient link between New Zealand's short-tailed bat and South American noctilionoid bats. Mol Phylogenet Evol 28:308-319.
40. Wolf YI, Rogozin IB, Koonin EV. 2004. Coelomata and not ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res 14:29-36.
41. Yang ZH. 1996. Maximum-likelihood models for combined analyses of multiple sequence data. J Mol Evol 42:587-596.