[1] | Dawkins R (2003) A devil's chaplain. New York: Houghton Mifflin.
|
[2] | Cracraft J, Donoghue MJ (2004) Assembling the tree of life. Oxford: Oxford University Press. editors.
|
[3] | Nishihara H, Satta Y, Nikaido M, Thewissen JGM, Stanhope MJ, et al. (2005) A retroposon analysis of Afrotherian phylogeny. Mol Biol Evol 22: 1823–1833.
|
[4] | Beverley SM, Wilson AC (1985) Ancient origin for Hawaiian Drosophilinae inferred from protein comparisons. Proc Natl Acad Sci USA 82: 4753–4757.
|
[5] | Philippe H, Lartillot N, Brinkmann H (2005) Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa and Protostomia. Mol Biol Evol 22: 1246–1253.
|
[6] | Philip GK, Creevey CJ, McInerney JO (2005) The Opisthokonta and the Ecdysozoa may not be clades: Stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa. Mol Biol Evol 22: 1175–1184.
|
[7] | Lockhart PJ, Penny D (2005) The place of within the radiation of angiosperms. Trends Plant Sci 10: 201–202.
|
[8] | Takezaki N, Figueroa F, Zaleska-Rutczynska Z, Takahata N, Klein J (2004) The phylogenetic relationship of tetrapod, coelacanth, and lungfish revealed by the sequences of 44 nuclear genes. Mol Biol Evol 21: 1512–1524.
|
[9] | Wolf YI, Rogozin IB, Koonin EV (2004) Coelomata and not Ecdysozoa: Evidence from genome-wide phylogenetic analysis. Genome Res 14: 29–36.
|
[10] | Dopazo H, Dopazo J (2005) Genome-scale evidence of the nematode-arthropod clade. Genome Biol 6: R41.
|
[11] | Matus DQ, Copley RR, Dunn CW, Hejnol A, Eccleston H, et al. (2006) Broad taxon and gene sampling indicate that chaetognaths are protostomes. Curr Biol 16: R575–576.
|
[12] | Marletaz F, Martin E, Perez Y, Papillon D, Caubit X, et al. (2006) Chaetognath phylogenomics: A protostome with deuterostome-like development. Curr Biol 16: R577–578.
|
[13] | Budd GE, Jensen S (2000) A critical reappraisal of the fossil record of the bilaterian phyla. Biol Rev 75: 253–295.
|
[14] | Simpson GG (1953) The major features of evolution. New York: Columbia University Press.
|
[15] | Fiala KI, Sokal RR (1985) Factors determining the accuracy of cladogram estimation: evaluation using computer simulation. Evolution 39: 609–622.
|
[16] | Lanyon SM (1988) The stochastic mode of molecular evolution: What consequences for systematic investigations? Auk 105: 565–573.
|
[17] | Huelsenbeck JP (1995) Performance of phylogenetic methods in simulation. Syst Biol 44: 17–48.
|
[18] | Felsenstein J (2003) Inferring phylogenies. Sunderland (Massachussetts): Sinauer.
|
[19] | Nikaido M, Rooney AP, Okada N (1999) Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: Hippopotamuses are the closest extant relatives of whales. Proc Natl Acad Sci USA 96: 10261–10266.
|
[20] | Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284: 2124–2129.
|
[21] | Gogarten JP (2003) Gene transfer: Gene swapping craze reaches eukaryotes. Curr Biol 13: R53–54.
|
[22] | Degnan JH, Rosenberg NA (2006) Discordance of species trees with their most likely gene trees. PLoS Genetics 2(5): e68. DOI: 10.1371/journal.pgen.0020068.
|
[23] | Arnold ML (1997) Natural hybridization and evolution. Oxford: Oxford University Press.
|
[24] | Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D (2006) Genetic evidence for complex speciation of humans and chimpanzees. Nature 441: 1103–1108.
|
[25] | Satta Y, Klein J, Takahata N (2000) DNA archives and our nearest relative: The trichotomy problem revisited. Mol Phylog Evol 14: 259–275.
|
[26] | Chen FC, Li WH (2001) Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am J Hum Genet 68: 444–456.
|
[27] | Salem AH, Ray DA, Xing JC, Callinan PA, Myers JS, et al. (2003) Alu elements and hominid phylogenetics. Proc Natl Acad Sci USA 100: 12787–12791.
|
[28] | Jennings WB, Edwards SV (2005) Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution 59: 2033–2047.
|
[29] | Rokas A, Williams BL, King N, Carroll SB (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798–804.
|
[30] | 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.
|
[31] | Murata Y, Nikaido M, Sasaki T, Cao Y, Fukumoto Y, et al. (2003) Afrotherian phylogeny as inferred from complete mitochondrial genomes. Mol Phylogenet Evol 28: 253–260.
|
[32] | Clack JA (2002) Gaining ground: The origin and evolution of tetrapods. Bloomington: Indiana University Press.
|
[33] | Rokas A, Kruger D, Carroll SB (2005) Animal evolution and the molecular signature of radiations compressed in time. Science 310: 1933–1938.
|
[34] | Zhang J, Kumar S (1997) Detection of convergent and parallel evolution at the amino acid sequence level. Mol Biol Evol 14: 527–536.
|
[35] | O'Huigin C, Satta Y, Takahata N, Klein J (2002) Contribution of homoplasy and of ancestral polymorphism to the evolution of genes in anthropoid primates. Mol Biol Evol 19: 1501–1513.
|
[36] | Naylor GJP, Brown WM (1997) Structural biology and phylogenetic estimation. Nature 388: 527–528.
|
[37] | Hickey DA, Singer GA (2004) Genomic and proteomic adaptations to growth at high temperature. Genome Biol 5: 117.
|
[38] | Pupko T, Galtier N (2002) A covarion-based method for detecting molecular adaptation: Application to the evolution of primate mitochondrial genomes. Proc R Soc Lond B Biol Sci 269: 1313–1316.
|
[39] | Felsenstein J (1978) Cases in which parsimony and compatibility methods will be positively misleading. Syst Zool 27: 401–410.
|
[40] | Averof M, Rokas A, Wolfe KH, Sharp PM (2000) Evidence for a high frequency of simultaneous double-nucleotide substitutions. Science 287: 1283–1286.
|
[41] | Gillespie JH (1991) The causes of molecular evolution. Oxford: Oxford University Press.
|
[42] | Sanderson MJ, Shaffer HB (2002) Troubleshooting molecular phylogenetic analyses. Annu Rev Ecol Syst 33: 49–72.
|
[43] | Wells RS (1996) Excessive homoplasy in an evolutionarily constrained protein. Proc R Soc Lond B Biol Sci 263: 393–400.
|
[44] | Smith NG, Eyre-Walker A (2002) Adaptive protein evolution in Drosophila. Nature 415: 1022–1024.
|
[45] | Fay JC, Wyckoff GJ, Wu CI (2002) Testing the neutral theory of molecular evolution with genomic data from . Nature 415: 1024–1026.
|
[46] | Chamary JV, Parmley JL, Hurst LD (2006) Hearing silence: Non-neutral evolution at synonymous sites in mammals. Nat Rev Genet 7: 98–108.
|
[47] | Bazin E, Glemin S, Galtier N (2006) Population size does not influence mitochondrial genetic diversity in animals. Science 312: 570–572.
|
[48] | Wang HC, Xia X, Hickey D (2006) Thermal adaptation of the small subunit ribosomal RNA gene: A comparative study. J Mol Evol 63: 120–126.
|
[49] | Bull JJ, Badgett MR, Wichman HA, Huelsenbeck JP, Hillis DM, et al. (1997) Exceptional convergent evolution in a virus. Genetics 147: 1497–1507.
|
[50] | Hillis DM (1996) Inferring complex phylogenies. Nature 383: 130–131.
|
[51] | Graybeal A (1998) Is it better to add taxa or characters to a difficult phylogenetic problem? Syst Biol 47: 9–17.
|
[52] | Rokas A, Carroll SB (2005) More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol Biol Evol 22: 1337–1344.
|
[53] | Rosenberg MS, Kumar S (2001) Incomplete taxon sampling is not a problem for phylogenetic inference. Proc Natl Acad Sci U S A 98: 10751–10756.
|
[54] | Kim J (1998) Large-scale phylogenies and measuring the performance of phylogenetic estimators. Syst Biol 47: 43–60.
|
[55] | Steel M, Hendy MD, Penny D (1998) Reconstructing phylogenies from nucleotide pattern probabilities: A survey and some new results. Discrete Appl Math 88: 367–396.
|
[56] | Hoelzer GA, Melnick DJ (1994) Patterns of speciation and limits to phylogenetic resolution. Trends Ecol Evol 9: 104–107.
|
[57] | Abouheif E, Zardoya R, Meyer A (1998) Limitations of metazoan 18S rRNA sequence data: Implications for reconstructing a phylogeny of the animal kingdom and inferring the reality of the Cambrian explosion. J Mol Evol 47: 394–405.
|
[58] | (2005) How much can evolved characters tell us about the tree that generated them. In: Gascuel O, editor. Mathematics of evolution and phylogeny. New York: Oxford University Press. pp. 384–412. editor.
|
[59] | Huelsenbeck JP, Rannala B (1997) Phylogenetic methods come of age: Testing hypotheses in an evolutionary context. Science 276: 227–232.
|
[60] | Penny D, McComish BJ, Charleston MA, Hendy MD (2001) Mathematical elegance with biochemical realism: The covarion model of molecular evolution. J Mol Evol 53: 711–723.
|
[61] | Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: 2310–2314.
|
[62] | Rokas A, Holland PWH (2000) Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol 15: 454–459.
|
[63] | Sanderson MJ (2005) Where have all the clades gone? A systematist's take on Inferring Phylogenies. Evolution 59: 2056–2058.
|
[64] | Shubin NH, Daeschler EB, Jenkins FA Jr (2006) The pectoral fin of and the origin of the tetrapod limb. Nature 440: 764–771.
|
[65] | Daeschler EB, Shubin NH, Jenkins FA Jr (2006) A Devonian tetrapod-like fish and the evolution of the tetrapod body plan. Nature 440: 757–763.
|
[66] | Ohno S (1996) The notion of the Cambrian pananimalia genome. Proc Natl Acad Sci U S A 93: 8475–8478.
|
[67] | Nichols SA, Dirks W, Pearse JS, King N (2006) Early evolution of animal cell signaling and adhesion genes. Proc Natl Acad Sci U S A 103: 12451–12456.
|
[68] | Kusserow A, Pang K, Sturm C, Hrouda M, Lentfer J, et al. (2005) Unexpected complexity of the gene family in a sea anemone. Nature 433: 156–160.
|
[69] | Venkatesh B, Erdmann MV, Brenner S (2001) Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates. Proc Natl Acad Sci USA 98: 11382–11387.
|