Functional genomics and the study of development, variation and evolution (original) (raw)

• Lewontin, R. C. The Genetic Basis of Evolutionary Change (Columbia Univ. Press, New York, 1974). Lewontin's treatment of the fundamental outstanding issues in evolutionary genetics is often more relevant today than it was 25 years ago. Particularly in his lament about the lack of a genotype-to-phenotype map, only now can we envisage providing the experimental data that will fill the gap raised in this classic book.
  Google Scholar
• Waddington, C. H. The Strategy of the Genes: a Discussion of Some Aspects of Theoretical Biology (George Allen and Unwin Ltd, 1957).
  Google Scholar
• Huxley, J. Evolution: The Modern Synthesis (Harper & Brothers, London, 1942).
• Dobzhansky, Th. G. Genetics and the Origin of Species (Columbia Univ. Press, New York, 1937). This text, along with aspects of Fisher's The Genetical Theory of Natural Selection seven years earlier, provided the basis for the neoDarwinian synthesis.
  Google Scholar
• Wright, S. Evolution and the Genetics of Populations (Chicago Univ. Press, Chicago, Illinois, 1968–1978).
  Google Scholar
• Hartl, D. L. & Clark, A. G. Principles of Population Genetics (Sinauer Associates, Sunderland, Massachusetts, 1997).
  Google Scholar
• Kreitman, M. & Comeron, J. M. Coding sequence evolution. Curr. Opin. Genet. Dev. 9, 637–641 (1999).
  Article CAS PubMed Google Scholar
• Kondrashov, A. S. Comparative genomics and evolutionary biology. Curr. Opin. Genet. Dev. 9, 624–629 (1999).
  Article CAS PubMed Google Scholar
• Fisher, R. A. The Genetical Theory of Natural Selection 2nd edn (Dover, New York, 1958).
  Google Scholar
• Eshel, I. & Feldman, M. W. On evolutionary genetic stability of the sex ratio. Theor. Popul. Biol. 21, 430–439 (1982).
  Article Google Scholar
• Wagner, G. P. What is the promise of developmental evolution? I. Why is developmental biology necessary to explain evolutionary innovations? J. Exp. Zool. 288, 95–98 (2000).
  Article CAS PubMed Google Scholar
• Mezey, J. G., Cheverud, J. M. & Wagner, G. P. Is the genotype–phenotype map modular? A statistical approach using mouse quantitative trait loci data. Genetics 156, 305–311(2000).
  CAS PubMed PubMed Central Google Scholar
• Sucena, E. & Stern, D. L. Divergence of larval morphology between Drosophila sechellia and its sibling species caused by _cis_-regulatory evolution of ovo/shaven-baby. Proc. Natl Acad. Sci. USA 97, 4530–4534 (2000).
  Article CAS PubMed PubMed Central Google Scholar
• Kopp, A., Duncan, I. & Carroll, S. B. Genetic control and evolution of sexually dimorphic characters in Drosophila. Nature 408, 553–559 (2000).
  Article CAS PubMed Google Scholar
• Kearsey, M. J. & Pooni, H. S. The Genetical Analysis of Quantitative Traits (Chapman & Hall, London, 1996).
  Book Google Scholar
• Falconer, D. S. & MacKay, T. F. C. Introduction to Quantitative Genetics (Wiley, New York, 1996).
  Google Scholar
• Risch, N. J. Searching for genetic determinants in the new millennium. Nature 405, 847–856 (2000).
  Article CAS PubMed Google Scholar
• Mackay, T. F. C. Quantitative trait loci in Drosophila. Nature Rev. Genet. 2, 11–20 (2001).
  Article CAS PubMed Google Scholar
• Mackay, T. F. C. & Langley, C. H. Molecular and phenotypic variation in the Achaete-scute region of Drosophila melanogaster. Nature 348, 64–66 (1990). Shows an important experimental model for correlating naturally occurring molecular genetic polymorphisms with phenotypic polymorphisms using candidate loci known to be involved in the development of the structures (bristles) being scored.
  Article CAS PubMed Google Scholar
• Lai, C., Lyman, R. F., Long, A. D., Langley, C. H. & Mackay, T. F. C. Naturally occurring variation in bristle number and DNA polymorphisms at the scabrous locus of Drosophila melanogaster. Science 266, 1697–1702 (1994).
  Article CAS PubMed Google Scholar
• Doebley, J., Stec, A. & Gustus, C. teosinte branched 1 and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics 141, 333–346 (1995).
  CAS PubMed PubMed Central Google Scholar
• Doebley, J., Stec, A. & Hubbard, L. The evolution of apical dominance in maize. Nature 386, 485–488 (1997).
  Article CAS PubMed Google Scholar
• Schena, M., Shalon, D., Davis, R. W. & Brown, P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470 (1995).
  Article CAS PubMed Google Scholar
• Shalon, D., Smith, S. J. & Brown, P. O. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6, 639–645 (1996).
  Article CAS PubMed Google Scholar
• Lockhart, D. J. et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnol. 14, 1675–1680 (1996).
  Article CAS Google Scholar
• DeRisi, J. L., Iyer, V. R. & Brown, P. O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680–686 (1997). This application of microarray-based transcriptional profiling to the study of metabolic flux stimulated many other researchers to consider using functional genomics approaches to assist their own biological problems.
  Article CAS PubMed Google Scholar
• Chu, S. et al. The transcriptional program of sporulation in budding yeast. Science 282, 699–705 (1998).
  Article CAS PubMed Google Scholar
• White, K. P., Rifkin, S. A., Hurban, P. & Hogness, D. S. Microarray analysis of Drosophila development during metamorphosis. Science 286, 2179–2184 (1999).
  Article CAS PubMed Google Scholar
• Reinke, V. et al. A global profile of germline gene expression in C. elegans. Mol. Cell 6, 605–616 (2000).
  Article CAS PubMed Google Scholar
• Eisen, M. B., Spellman, P. T., Brown, P. O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA 95, 14863–14868 (1998).
  Article CAS PubMed PubMed Central Google Scholar
• Tamayo, P. et al. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc. Natl Acad. Sci. USA 96, 2907–2912 (1999).
  Article CAS PubMed PubMed Central Google Scholar
• Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306–2309 (2000). This paper, along with a similar one by Iyer et al . published a month later in Nature , showed the feasibility of mapping DNA–protein interactions genome-wide and combining such information with transcriptional profiling. Integration of several types of functional genomic data promises to help resolve complex genetic networks.
  Article CAS PubMed Google Scholar
• Iyer, V. R. et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409, 533–538 (2001).
  Article CAS PubMed Google Scholar
• Van Steensel, B., Delrow, J. & Henikoff, S. Chromatin profiling using targeted DNA adenine methyltransferase. Nature Genet. 27, 304–308 (2001).
  Article CAS PubMed Google Scholar
• Ideker, O. Integrating genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929–934 (2001).
  Article CAS PubMed Google Scholar
• Hartemink, A. J., Gifford, D. K., Jaakkola, T. S. & Young, R. A. Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pac. Symp. Biocomput. 422–433 (2001).
• Orr, H. A. & Presgraves, D. C. Speciation by postzygotic isolation: forces, genes and molecules. Bioessays 22, 1085–1094 (2000). A recent and thorough review of the genetics of postzygotic isolation.
  Article CAS PubMed Google Scholar
• Hollocher, H. & Wu, C. I. The genetics of reproductive isolation in the Drosophila simulans clade: X vs. autosomal effects and male vs. female effects. Genetics 143, 1243–1255 (1996).
  CAS PubMed PubMed Central Google Scholar
• Ting, C. T., Tsaur, S. C., Wu, M. L. & Wu, C. I. A rapidly evolving homeobox at the site of a hybrid sterility gene. Science 282, 1501–1504 (1998).
  Article CAS PubMed Google Scholar
• Meyer, A., Kocher, T. D., Basasibwaki, P. & Wilson, A. C. Monophyletic origin of Lake Victoria cichlid fishes suggested by mitochondrial DNA sequences. Nature 347, 550–553 (1990).
  Article CAS PubMed Google Scholar
• Sturmbauer, C. & Meyer, A. Genetic divergence, speciation and morphological stasis in a lineage of African cichlid fishes. Nature 358, 578–581 (1992).
  Article CAS PubMed Google Scholar
• Grant, P. R. & Grant, B. R. Genetics and the origin of bird species. Proc. Natl Acad. Sci. USA 94, 7768–7775 (1997).
  Article CAS PubMed PubMed Central Google Scholar
• Myers, E. W. et al. A whole-genome assembly of Drosophila. Science 287, 2196–2204 (2000).
  Article CAS PubMed Google Scholar
• Powell, J. R., Caccone, A., Gleason, J. M. & Nigro, L. Rates of DNA evolution in Drosophila depend on function and developmental stage of expression. Genetics 133, 291–298 (1993).
  CAS PubMed PubMed Central Google Scholar
• Kliman, R. M. et al. The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics 156, 1913–1931 (2000).
  CAS PubMed PubMed Central Google Scholar
• Schmid, K. J. & Tautz, D. A screen for fast evolving genes from Drosophila. Proc. Natl Acad. Sci. USA 94, 9746–9750 (1997).
  Article CAS PubMed PubMed Central Google Scholar
• Horn, C. & Wimmer, E. A. A versatile vector set for animal transgenesis. Dev. Genes Evol. 210, 630–637 (2000).
  Article CAS PubMed Google Scholar
• MacDowell, E. C. Bristle inheritance in Drosophila. II. Selection. J. Exp. Zool. 30, 419–460 (1917).
  Article Google Scholar
• Sturtevant, A. H. An Analysis of the Effects of Selection (Publication 264, Carnegie Institute of Washington, 1918).
  Google Scholar
• Payne, F. The effect of artificial selection on bristle number in Drosophila ampelophila and its interpretation. Proc. Natl Acad. Sci. USA 4, 55–58 (1918).
  Article CAS PubMed PubMed Central Google Scholar
• Flexon, P. B. & Rodell, C. F. Genetic recombination and directional selection for DDT resistance in Drosophila melanogaster. Nature 298, 672–674 (1982).
  Article CAS PubMed Google Scholar
• Hirsch, J. & Erlenmyer-Kimling, L. Sign of taxis as a property of the genotype. Science 134, 835–836 (1961).
  Article CAS PubMed Google Scholar
• Dobzhansky, Th. & Spassky, B. Artificial and natural selection for two behavioral traits in Drosophila pseudoobscura. Proc. Natl Acad. Sci. USA 62, 75–80 (1969). An important demonstration of the malleability of complex, and in this case behavioural, traits under selection in Drosophila.
  Article CAS PubMed PubMed Central Google Scholar
• Joshi, A., Knight, C. D. & Mueller, L. D. Genetics of larval urea tolerance in Drosophila melanogaster. Heredity 77, 33–39 (1996).
  Article PubMed Google Scholar
• Mueller, L. D. Evolution of competitive ability in Drosophila by density-dependent natural selection. Proc. Natl Acad. Sci. USA 85, 4383–4386 (1988).
  Article CAS PubMed PubMed Central Google Scholar
• Rose, M. R. Genetics of increased lifespan in Drosophila. Bioessays 11, 132–135 (1989).
  Article CAS PubMed Google Scholar
• Partridge, L., Prowse, N. & Pignatelli, P. Another set of responses and correlated responses to selection on age at reproduction in Drosophila melanogaster. Proc. R. Soc. Lond. B 266, 255–261 (1999).
  Article CAS Google Scholar
• Stearns, S. C. Life history evolution: successes, limitations, and prospects. Naturwissenschaften 87, 476–486 (2000).
  Article CAS PubMed Google Scholar
• Villares, R. & Cabrera, C. V. The Achaete-scute gene complex of D. melanogaster: conserved domains in a subset of genes required for neurogenesis and their homology to myc. Cell 50, 415–424 (1987).
  Article CAS PubMed Google Scholar
• Powell, P. A., Wesley, C., Spencer, S. & Cagan, R. L. Scabrous complexes with Notch to mediate boundary formation. Nature 409, 626–630 (2001).
  Article CAS PubMed Google Scholar
• Long, A. D. et al. High resolution mapping of genetic factors affecting abdominal bristle number in Drosophila melanogaster. Genetics 139, 1273–1291 (1995).
  CAS PubMed PubMed Central Google Scholar
• Amlou, M., Moreteau, B. & David, J. R. Larval tolerance in the Drosophila melanogaster species complex toward the two toxic acids of the D. sechellia host plant. Hereditas 129, 7–14 (1998).
  Article CAS PubMed Google Scholar
• Jones, C. D. The genetic basis of Drosophila sechellia's resistance to a host plant toxin. Genetics 149, 1899–1908 (1998).
  CAS PubMed PubMed Central Google Scholar
• Haff, L. A. & Smirnov, I. P. Single-nucleotide polymorphism identification assays using a thermostable DNA polymerase and delayed extraction MALDI-TOF mass spectrometry. Genome Res. 7, 378–388 (1997).
  Article CAS PubMed PubMed Central Google Scholar
• Cai, H. et al. Flow cytometry-based minisequencing: a new platform for high-throughput single-nucleotide polymorphism scoring. Genomics 66, 135–143 (2000).
  Article CAS PubMed Google Scholar
• Ronaghi, M., Uhlen, M. & Nyren, P. A sequencing method based on real-time pyrophosphate. Science 281, 363–365 (1998).
  Article CAS PubMed Google Scholar
• Chee, M. et al. Accessing genetic information with high-density DNA arrays. Science 274, 610–614 (1996).
  Article CAS PubMed Google Scholar
• Zhong, X. B., Lizardi, P. M., Huang, X. H., Bray-Ward, P. L. & Ward, D. C. Visualization of oligonucleotide probes and point mutations in interphase nuclei and DNA fibers using rolling circle DNA amplification. Proc. Natl Acad. Sci. USA 98, 3940–3945 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Lyamichev, V. et al. Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nature Biotechnol. 17, 292–296 (1999).
  Article CAS Google Scholar
• Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
  Article CAS PubMed Google Scholar
• Dobzhansky, Th. Studies on hybrid sterility. II. Localization of sterility factors in Drosophila psuedoobscura hybrids. Genetics 21, 113–135 (1936).
  CAS PubMed PubMed Central Google Scholar
• Prakash, S. Origin of reproductive isolation in the absence of apparent genic differentiation in a geographic isolate of Drosophila pseudoobscura. Genetics 72, 143–155 (1972).
  CAS PubMed PubMed Central Google Scholar
• Noor, M. A. Speciation driven by natural selection in Drosophila. Nature 375, 674–675 (1995).
  Article CAS PubMed Google Scholar
• Travisano, M., Mongold, J. A., Bennett, A. F. & Lenski, R. E. Experimental tests of the roles of adaptation, chance, and history in evolution. Science 267, 87–90 (1995).
  Article CAS PubMed Google Scholar
• Elena, S. F., Cooper, V. S. & Lenski, R. E. Punctuated evolution caused by selection of rare beneficial mutations. Science 272, 1802–1804 (1996).
  Article CAS PubMed Google Scholar
• Arjan, J. A. et al. Diminishing returns from mutation supply rate in asexual populations. Science 283, 404–406 (1999).
  Article CAS PubMed Google Scholar
• Paquin, C. & Adams, J. Frequency of fixation of adaptive mutations is higher in evolving diploid than haploid yeast populations. Nature 302, 495–500 (1983).
  Article CAS PubMed Google Scholar
• Ferea, T. L., Botstein, D., Brown, P. O. & Rosenzweig, R. F. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl Acad. Sci. USA 96, 9721–9726 (1999).
  Article CAS PubMed PubMed Central Google Scholar
• Riehle, M. M., Bennett, A. F. & Long, A. D. Genetic architecture of thermal adaptation in Escherichia coli. Proc. Natl Acad. Sci. USA 98, 525–530 (2001).
  Article CAS PubMed PubMed Central Google Scholar