Estimating the tempo and mode of gene family evolution from comparative genomic data

Genome Research

Volumn 15, Issue 8, 2005, Pages 1153-1160

  Hahn, Matthew W ^a   De Bie, Tijl ^c   Stajich, Jason E ^d   Nguyen, Chi ^b   Cristianini, Nello ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of California Davis   (United States)

^c UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^d DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIRTH; DEATH; GENE DELETION; GENE DUPLICATION; GENETIC VARIABILITY; GENOME; GENOME ANALYSIS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MULTIGENE FAMILY; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; STATISTICAL MODEL; STOCHASTIC MODEL; YEAST;

EVOLUTION, MOLECULAR; GENOMICS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MULTIGENE FAMILY; PHYLOGENY; SACCHAROMYCES; STOCHASTIC PROCESSES;

EID: 23744452485     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.3567505     Document Type: Article

References (53)

1. Abril, J.F., Agarwal, P., Alexandersson, M., Antonarakis, S.E., Baertsch, R., Berry, E., Birney, E., Bork, P., Bray, N., Brent, M.R., et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
2. Bailey, N. 1964. The elements of stochastic processes. John Wiley & Sons, Inc., New York.
3. Berger, R.L. and Boos, D.D. 1994. P values maximized over a confidence set for the nuisance parameter. J. Amer. Statist. Assoc. 89: 1012-1016.
4. Cliften, P., Sudarsanam, P., Desikan, A., Fulton, L., Fulton, B., Majors, J., Waterston, R., Cohen, B.A., and Johnston, M. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
5. Copley, R., Goodstadt, L., and Ponting, C. 2003. Eukaryotic domain evolution inferred from genome comparisons. Curr. Opin. Genet. Dev. 13: 623-628.
6. Darwin, J.H. 1956. The behaviour of an estimator for a simple birth and death process. Biometrika 43: 23-31.
7. Demortier, L. 2003. Constructing ensembles of pseudo-experiments. In Proceedings of PHYSTAT2003: Statistical problems in particle physics, astrophysics, and cosmology (eds. L. Lyons, et al.), pp. 256-260. Stanford Linear Accelerator Center, Stanford, CA.
8. Enright, A.J., Van Dongen, S., and Ouzounis, C.A. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30: 1575-1584.
9. Feller, W. 1968. An introduction to probability theory and its applications. John Wiley & Sons, Inc., New York.
10. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17: 368-376.
11. Friedman, R. and Hughes, A.L. 2001. Gene duplication and the structure of eukaryotic genomes. Genome Res. 11: 373-381.
12. Garczarek, L., Hess, W., Hotzendorff, J., Staay, G.V.D., and Partensky, F. 2000. Multiplication of antenna genes as a major adaptation to low light in a marine prokaryote. Proc. Natl. Acad. Sci. 97: 4098-4101.
13. Gu, X. and Zhang, H. 2004. Genome phylogeny inference based on gene contents. Mol. Biol. Evol. 21: 1401-1408.
14. Harvey, P.H. and Pagel, M.D. 1991. The comparative method in evolutionary biology. Oxford University Press, Oxford, UK.
15. Holt, R.A., Subramanian, G.M., Halpern, A., Sutton, G.G., Charlab, R., Nusskern, D.R., Wincker, P., Clark, A.G., Ribeiro, J.M.C., Wides, R., et al. 2002. The genome sequence of the malaria mosquito Anopheles gambiae. Science 298: 129-149.
16. Huynen, M.A. and van Nimwegen, E. 1998. The frequency distribution of gene family sizes in complete genomes. Mol. Biol. Evol. 15: 583-589.
17. Jin, Y.L. and Speers, R.A. 1998. Flocculation of Saccharomyces cerevisiae. Food Res. Int. 31: 421-440.
18. Karev, G.P., Wolf, Y.I., Rzhetsky, A.Y., Berezovskaya, F.S., and Koonin, E.V. 2002. Birth and death of protein domains: A simple model of evolution explains power law behavior. BMC Evol. Biol. 2: 18.
19. Kellis, M., Patterson, N., Endrizzi, M., Birren, B.W., and Lander, E.S. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
20. Kellis, M., Birren, B.W., and Lander, E.S. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617-624.
21. Kidwell, M.G. 2002. Transposable elements and the evolution of genome size in eukaryotes. Genetica 115: 49-63.
22. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
23. Lauritzen, S.L. 1996. Graphical models. Clarendon Press, Oxford, UK.
24. Lehmann, E.L. 1959. Testing statistical hypotheses, chap. 3. John Wiley & Sons, Inc., New York.
25. Leonardo, T.E. and Nuzhdin, S.V. 2002. Intracellular battlegrounds: Conflict and cooperation between transposable elements. Genet. Res. 80: 155-161.
26. Lespinet, O., Wolf, Y., Koonin, E., and Aravind, L. 2002. The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res. 12: 1048-1059.
27. Li, W.-H. 1997. Molecular evolution. Sinauer Associates, Sunderland, MA.
28. Lindsey, J.K. 1996. Parametric statistical inference. Oxford University Press, Oxford, UK.
29. Lutfalla, G., Crollius, H.R., Strange-Thomann, N., Jaillon, O., Mogensen, K., and Monneron, D. 2003. Comparative genomic analysis reveals independent expansion of a lineage-specific gene family in vertebrates: The class II cytokine receptors and their ligands in mammals and fish. BMC Genomics 4: 29.
30. Lynch, M. and Conery, J.S. 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
31. -. 2003. The evolutionary demography of duplicate genes. J. Struct. Funct. Genomics 3: 35-44.
32. Mooers, A.O. and Schluter, D. 1998. Fitting macroevolutionary models to phylogenies: An example using vertebrate body sizes. Contr. Zool. 68: 3-18.
33. Nei, M., Gu, X., and Sitnikova, T. 1997. Evolution by the birth-and-death process in multigene families of the vertebrate immune system. Proc. Natl. Acad. Sci. 94: 7799-7806.
34. Oakeshott, J., Claudianos, C., Russell, R., and Robin, G. 1999. Carboxyl/cholinesterases: A case study of the evolution of a successful multigene family. Bioessays 21: 1031-1042.
35. Pagel, M.D. 1999. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst. Biol. 48: 612-622.
36. Pearl, J. 1988. Probabilistic reasoning in intelligent systems: Networks of plausible inference. Morgan Kaufmann, San Mateo, CA.
37. Qian, J., Luscombe, N.M., and Gerstein, M. 2001. Protein family and fold occurrence in genomes: Power-law behaviour and evolutionary model. J. Mol. Biol. 313: 673-681.
38. Ranson, H., Claudianos, C., Ortelli, F., Abgrall, C., Hemingway, J., Sharakhova, M.V., Unger, M.F., Collins, F.H., and Feyereisen, R. 2002. Evolution of supergene families associated with insecticide resistance. Science 298: 179-181.
39. Reed, W.J. and Hughes, B.D. 2004. A model explaining the size distribution of gene and protein families. Math. Biosci. 189: 97-102.
40. Rokas, A., Williams, B.L., King, N., and Carroll, S.B. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804.
41. Sims, H.J. and McConway, K.J. 2003. Nonstochastic variation of species-level diversification rates within angiosperms. Evolution 57: 460-479.
42. Slatkin, M. and Rannala, B. 1997. Estimating the age of alleles by use of intrallelic variability. Am. J. Hum. Genet. 60: 447-458.
43. Snel, B., Bork, P., and Huynen, M. 2002. Genomes in flux: The evolution of archaeal and proteobacterial gene content. Genome Res. 12: 17-25.
44. Stein, L.D., Bao, Z.R., Blasiar, D., Blumenthal, T., Brent, M.R., Chen, N.S., Chinwalla, A., Clarke, L., Clee, C., Coghlan, A., et al. 2003. The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics. PLoS Biology 1: 166-192.
45. Szathmary, E., Jordan, F., and Pal, C. 2001. Can genes explain biological complexity? Science 292: 1315-1316.
46. Tatusov, R., Koonin, E., and Lipman, D. 1997. A genomic perspective on protein families. Science 278: 631-637.
47. Theissen, U., Hoffmeister, M., Grieshaber, M., and Martin, W. 2003. Single eubacterial origin of eukaryotic sulfide:quinone oxidoreductase, a mitochondrial enzyme conserved from the early evolution of eukaryotes during anoxic and sulfidic times. Mol. Biol. Evol. 20: 1564-1574.
48. Van Dongen, S. 2000. A cluster algorithm for graphs. Technical Report INS-R0010, National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam.
49. Wang, R.L., Stec, A., Hey, J., Lukens, L., and Doebley, J. 1999. The limits of selection during maize domestication. Nature 398: 236-239.
50. Yanai, I., Camacho, C.J., and DeLisi, C. 2000. Predictions of gene family distributions in microbial genomes: Evolution by gene duplication and modification. Phys. Rev. Lett. 85: 2641-2644.
51. Yang, Z. and Bielawski, J. 2000. Statistical methods for detecting molecular evolution. Trends Ecol. Evol. 15: 496-503.
52. Zhang, H. and Gu, X. 2004. Maximum likelihood for genome phylogeny on gene content. Stat. Appl. Genet. Mol. Biol. 3: Article 31.
53. Zwickl, D.J. and Holder, M.T. 2004. Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. Systematic Biology 53: 877-888.