The evolution of genetic networks by non-adaptive processes (original) (raw)

• Gerhart, J. & Kirschner, M. Cells, Embryos and Evolution (Blackwell Science, Malden, 1997).
  Google Scholar
• Barab'asi, A. L. & Oltvai, Z. N. Network biology: understanding the cell's functional organization. Nature Rev. Genet. 5, 101–113 (2004).
  Article CAS Google Scholar
• Babu, M. M., Teichmann, S. A. & Aravind, L. Evolutionary dynamics of prokaryotic transcriptional regulatory networks. Mol. Biol. 358, 614–633 (2006).
  Article Google Scholar
• Balaji, S., Iyer, L. M., Aravind, L. & Babu, M. M. Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks. J. Mol. Biol. 360, 204–212 (2006).
  Article CAS PubMed Google Scholar
• Davidson, E. H. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution (Academic, New York, 2006).
  Google Scholar
• Alon, U. Biological networks: the tinkerer as an engineer. Science 301, 1866–1867 (2003).
  Article CAS PubMed Google Scholar
• Adami, C. Digital genetics: unravelling the genetic basis of evolution. Nature Rev. Genet. 7, 109–118 (2006).
  Article CAS PubMed Google Scholar
• Wagner, A. Does selection mold molecular networks? Science STKE 202, pe41 (2003). One of the first papers to raise questions about the adaptive paradigm for the architecture of genetic networks.
  Google Scholar
• Sole, R. V. & Valverde, S. Are network motifs the spandrels of cellular complexity? Trends Ecol. Evol. 21, 419–422 (2006).
  Article PubMed Google Scholar
• Keller, E. F. Revisiting 'scale-free' networks. Bioessays 27, 1060–1068 (2005).
  Article PubMed Google Scholar
• Lynch, M. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc. Natl Acad. Sci. USA 104, S8597–S8604 (2007). This paper raises questions about the rationale and objectivity of numerous arguments that nearly all aspects of molecular, cellular and developmental complexity have arisen by adaptive mechanisms.
  Article Google Scholar
• Wilkins, A. S. The Evolution of Developmental Pathways (Sinauer, Sunderland, 2002). An excellent overview of our knowledge (or lack thereof) of the evolutionary forces that mould developmental pathways.
  Google Scholar
• Lynch, M. The Origins of Genome Architecture (Sinauer, Sunderland, 2007).
  Google Scholar
• Davidson, E. H. & Erwin, D. H. Gene regulatory networks and the evolution of animal body plans. Science 311, 796–800 (2006).
  Article CAS PubMed Google Scholar
• Thieffry, D., Huerta, A. M., Perez-Rueda, E. & Collado-Vides, J. From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. Bioessays 20, 433–440 (1998).
  Article CAS PubMed Google Scholar
• Lee, T. I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799–804 (2002).
  Article CAS PubMed Google Scholar
• Wuchty, S. & Almaas, E. Evolutionary cores of domain co-occurrence networks. BMC Evol. Biol. 5, 24 (2005).
  Article PubMed PubMed Central Google Scholar
• Johnson, N. A. & Porter, A. H. Rapid speciation via parallel, directional selection on regulatory genetic pathways. J. Theor. Biol. 205, 527–542 (2000).
  Article CAS PubMed Google Scholar
• Force, A. et al. The origin of subfunctions and modular gene regulation. Genetics 170, 433–446 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Haag, E. S. & Molla, M. N. Compensatory evolution of interacting gene products through multifunctional intermediates. Evolution 59, 1620–1632 (2005).
  Article CAS PubMed Google Scholar
• Wagner, A. Robustness and Evolvability in Living Systems (Princeton Univ. Press, Princeton, 2005). A broad and relatively balanced view of the evolutionary mechanisms that can lead to the robustness of living systems to external and internal perturbations.
  Google Scholar
• Conant, G. C. & Wagner, A. Convergent evolution of gene circuits. Nature Genet. 34, 264–266 (2003).
  Article CAS PubMed Google Scholar
• Artzy-Randrup, Y., Fleishman, S. J., Ben-Tal, N. & Stone, L. Comment on 'Network motifs: simple building blocks of complex networks' and 'Superfamilies of evolved and designed networks'. Science 305, 1107 (2004).
  Article CAS PubMed Google Scholar
• van Noort, V., Snel, B. & Huynen, M. A. The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model. EMBO Rep. 5, 280–284 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• de Silva, E. & Stumpf, M. P. Complex networks and simple models in biology. J. R. Soc. Interface 2, 419–430 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Wilkins, A. S. Recasting developmental evolution in terms of genetic pathway and network evolution and the implications for comparative biology. Brain Res. Bull. 66, 495–509 (2005).
  Article PubMed Google Scholar
• Sommer, R. J. Evolution and development — the nematode vulva as a case study. Bioessays 19, 225–231 (1997).
  Article CAS PubMed Google Scholar
• Ludwig, M. Z., Bergman, C., Patel, N. H. & Kreitman, M. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403, 564–567 (2000).
  Article CAS PubMed Google Scholar
• Ruvinsky, I. & Ruvkun, G. Functional tests of enhancer conservation between distantly related species. Development 130, 5133–5142 (2003).
  Article CAS PubMed Google Scholar
• Coulson, R. M. & Ouzounis, C. A. The phylogenetic diversity of eukaryotic transcription. Nucleic Acids Res. 31, 653–660 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Goltsev, Y., Hsiong, W., Lanzaro, G. & Levine, M. Different combinations of gap repressors for common stripes in Anopheles and Drosophila embryos. Dev. Biol. 275, 435–446 (2004).
  Article CAS PubMed Google Scholar
• Coulson, R. M., Touboul, N. & Ouzounis, C. A. Lineage-specific partitions in archaeal transcription. Archaea 2, 117–125 (2006).
  Article PubMed Central Google Scholar
• Hill, R. C. et al. Genetic flexibility in the convergent evolution of hermaphroditism in Caenorhabditis nematodes. Dev. Cell 10, 531–538 (2006).
  Article CAS PubMed Google Scholar
• Mazurie, A., Bottani, S. & Vergassola, M. An evolutionary and functional assessment of regulatory network motifs. Genome Biol. 6, R35 (2005).
  Article PubMed PubMed Central Google Scholar
• Moses, A. M. et al. Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput.Biol. 2, 1219–1231 (2006).
  Article CAS Google Scholar
• Tsong, A. E., Tuch, B. B., Li, H. & Johnson, A. D. Evolution of alternative transcriptional circuits with identical logic. Nature 443, 415–420 (2006). An elegant demonstration of how dramatic changes in regulatory mechanisms can be brought about by intermediate, neutral steps involving functional redundancy.
  Article CAS PubMed Google Scholar
• Marino-Ramirez, L., Jordan, I. K. & Landsman, D. Multiple independent evolutionary solutions to core histone gene regulation. Genome Biol. 7, R122 (2006).
  Article PubMed PubMed Central Google Scholar
• Tanay, A., Regev, A. & Shamir, R. Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Proc. Natl Acad. Sci. USA 102, 7203–7208 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Lozada-Chavez, I., Janga, S. C. & Collado-Vides, J. Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res. 34, 3434–3445 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Perez-Rueda, E., Collado-Vides, J. & Segovia, L. Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Comput. Biol. Chem. 28, 341–350 (2004).
  Article CAS PubMed Google Scholar
• Riechmann, J. L. et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290, 2105–2110 (2000).
  Article CAS PubMed Google Scholar
• Messina, D. N., Glasscock, J., Gish, W. & Lovett, M. An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression. Genome Res. 14, 2041–2047 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Harbison, C. T. et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99–104 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Stone, J. R. & Wray, G. A. Rapid evolution of _cis_-regulatory sequences via local point mutations. Mol. Biol. Evol. 18, 1764–1770 (2001).
  Article CAS PubMed Google Scholar
• Hahn, M. W., Stajich, J. E. & Wray, G. A. The effects of selection against spurious transcription factor binding sites. Mol. Biol. Evol. 20, 901–906 (2003). This work shows that even non-functional DNA can be under selection for the avoidance of spurious regulatory sites
  Article CAS PubMed Google Scholar
• Shen-Orr, S. S., Milo, R., Mangan, S. & Alon, U. Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genet. 31, 64–68 (2002).
  Article CAS PubMed Google Scholar
• Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N. & Barabasi, A. L. The large-scale organization of metabolic networks. Nature 407, 651–654 (2000).
  Article CAS PubMed Google Scholar
• Rodriguez-Caso, C., Medina, M. A. & Sole, R. V. Topology, tinkering and evolution of the human transcription factor network. FEBS J. 272, 6423–6434 (2005).
  Article CAS PubMed Google Scholar
• Chung, F., Lu, L., Dewey, T. G. & Galas, D. J. Duplication models for biological networks. J. Comput. Biol. 10, 677–687 (2003).
  Article CAS PubMed Google Scholar
• Yuh, C. H., Bolouri, H. & Davidson, E. H. Genomic _cis_-regulatory logic: experimental and computational analysis of a sea urchin gene. Science 279, 1896–1902 (1998).
  Article CAS PubMed Google Scholar
• Balhoff, J. P. & Wray, G. A. Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites. Proc. Natl Acad. Sci. USA 102, 8591–8596 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Romano, L. A. & Wray, G. A. Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and _trans_-acting components of transcriptional regulation. Development 130, 4187–4199. References 51 and 52 provide dramatic evidence that typological descriptions of the regulatory structure of genes on the basis of narrow model systems ignore important aspects of variation that are found within and among natural populations.
• True, J. R. & Haag, E. S. Developmental system drift and flexibility in evolutionary trajectories. Evol. Dev. 3, 109–119 (2001). A thoughtful account of how major modifications of developmental processes can come about by neutral processes.
  Article CAS PubMed Google Scholar
• Soyer, O. S. & Bonhoeffer, S. Evolution of complexity in signaling pathways. Proc. Natl Acad. Sci. USA 103, 16337–16342 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• van Nimwegen, E. Scaling laws in the functional content of genomes. Trends Genet. 19, 479–484 (2003).
  Article CAS PubMed Google Scholar
• Clark, A. G. Invasion and maintenance of a gene duplication. Proc. Natl Acad. Sci. USA 91, 2950–2954 (1994).
  Article CAS PubMed PubMed Central Google Scholar
• Lynch, M., O'Hely, M., Walsh, B. & Force, A. The probability of fixation of a newly arisen gene duplicate. Genetics 159, 1789–1804 (2001).
  CAS PubMed PubMed Central Google Scholar
• Proulx, S. R. & Phillips, P. C. The opportunity for canalization and the evolution of genetic networks. Am. Nat. 165, 147–162 (2005). References 56 – 58 formally demonstrate the difficulties of evolving genetic redundancy by natural selection.
  Article PubMed Google Scholar
• Lynch, M. & Conery, J. S. The evolutionary fate and consequences of duplicate genes. Science 290, 1151–1154 (2000).
  Article CAS PubMed Google Scholar
• Wagner, A. The role of population size, pleiotropy and fitness effects of mutations in the evolution of overlapping gene functions. Genetics 154, 1389–1401 (2000).
  CAS PubMed PubMed Central Google Scholar
• Wagner, A. Robustness against mutations in genetic networks of yeast. Nature Genet. 24, 355–361 (2000).
  Article CAS PubMed Google Scholar
• Bhan, A., Galas, D. J. & Dewey, T. G. A duplication growth model of gene expression networks. Bioinformatics 18, 1486–1493 (2002).
  Article CAS PubMed Google Scholar
• Cordero, O. X. & Hogeweg, P. Feed-forward loop circuits as a side effect of genome evolution. Mol. Biol. Evol. 23, 1931–1936 (2006).
  Article CAS PubMed Google Scholar
• Foster, D. V., Kauffman, S. A., & Socolar, J. E. Network growth models and genetic regulatory networks. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 73, 031912 (2006).
  Article CAS PubMed Google Scholar
• Ciliberti, S., Martin, O. C. & Wagner, A. Robustness can evolve gradually in complex regulatory gene networks with varying topology. PLoS Comput. Biol. 3, e15 (2007).
  Article PubMed PubMed Central Google Scholar
• Pagel, M., Meade, A. & Scott, D. Assembly rules for protein networks derived from phylogenetic-statistical analysis of whole genomes. BMC Evol. Biol. 7, S16 (2007).
  Article PubMed PubMed Central Google Scholar
• Milo, R. et al. Network motifs: simple building blocks of complex networks. Science 298, 824–827 (2002).
  Article CAS PubMed Google Scholar
• Yeger-Lotem, E. et al. Network motifs in integrated cellular networks of transcription-regulation and protein–protein interaction. Proc. Natl Acad. Sci. USA 101, 5934–5939 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Carroll, S. B. Evolution at two levels: on genes and form. PLoS Biol. 3, e245 (2005). The author argues that most interesting aspects of evolution are associated with changes at the level of gene regulation, rather than with changes in coding DNA.
  Article PubMed PubMed Central Google Scholar
• Hoekstra, H. E. & Coyne, J. A. The locus of evolution: evo–devo and the genetics of adaptation. Evolution 61, 995–1016 (2007). This paper presents a counterview to reference 69.
  Article PubMed Google Scholar
• Crow, J. F. & Kimura, M. An Introduction to Population Genetics Theory (Harper & Row, New York, 1970).
  Google Scholar