by Nick Lane
Frank, A. C., Amiri, H., and Andersson, S. G. E. Genome deterioration: Loss of repeated sequences and accumulation of junk DNA. Genetica 115: 1–12; 2002.
Vellai, T., Takács, K., and Vida, G. A new aspect to the origin and evolution of eukaryotes. Journal of Molecular Evolution 46: 499–507; 1998.
—— Vida, G. The origin of eukaryotes: The difference between prokaryotic and eukaryotic cells. Proceedings of the Royal Society of London B: Biological Sciences 266: 1571–1577; 1999.
Difficulties in defining bacterial ‘species’
Doolittle, W. F., Boucher, Y., Nesbo, C. L, Douady, C. J., Andersson, J. O., and Roger, A. J. How big is the iceberg of which organellar genes in nuclear genomes are but the tip? Philosophical Transactions of the Royal Society of London B: Biological Sciences 358: 39–58; 2003.
Martin, W. Woe is the Tree of Life. In J. Sapp (ed.), Microbial Phylogeny and Evolution: Concepts and Controversies. Oxford University Press, New York, USA, 2005.
Maynard Smith, J., Feil, E. J., and Smith, N. H. Population structure and evolutionary dynamics of pathogenic bacteria. Bioessays 22: 1115–1122; 2000.
Spratt, B. G., Hanage, W. P., and Feil, E. J. The relative contributions of recombination and point mutation to the diversification of bacterial clones. Current Opinion in Microbiology 4: 602–606; 2001.
Respiratory efficiency and genome size
Konstantinidis, K., and Tiedje, J. M. Trends between gene content and genome size in prokaryotic species with larger genomes. Proceedings of the National Academy of Sciences USA 101: 3160–3165; 2004.
Vellai, T., Takács, K., and Vida, G. A new aspect to the origin and evolution of eukaryotes. Journal of Molecular Evolution 46: 499–507; 1998.
Giant bacteria
Schulz, H. N., Brinkhoff, T., Ferdelman, T. G., Hernández Mariné, M., Teske, A., and Jørgensen, B. B. Dense populations of a giant sulfur bacterium in Namibian shelf sediments. Science 284: 493–495; 1999.
Bacteria without cell walls
Ruepp, A., Graml, W., Santos-Martinez, M. L., Koretke, K. K., Volker, C., Mewes, H. W., Frishman, D., Stocker, S., Lupas, A. N., and Baumeister, W. The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature 407: 508–513; 2000.
Taylor-Robinson, D. Mycoplasma genitalium—an update. International Journal of STD and AIDS 13: 145–151; 2002.
Gene transfer to the nucleus
Bensasson, D., Feldman, M. W., and Petrov, D. A. Rates of DNA duplication and mitochondrial DNA insertion in the human genome. Journal of Molecular Evolution 57: 343–354; 2003.
Huang, C. Y., Ayliffe, M. A., and Timmis, J. N. Direct measurement of the transfer rate of chloroplast DNA into the nucleus. Nature 422: 72–76; 2003.
Martin, W. Gene transfer from organelles to the nucleus: Frequent and in big chunks. Proceedings of the National Academy of Sciences USA 100: 8612–8614; 2003.
Turner, C., Killoran, C., Thomas, N. S., Rosenberg, M., Chuzhanova, N. A., Johnston, J., Kemel, Y., Cooper, D. N., and Biesecker, L. G. Human genetic disease caused by de novo mitochondrial-nuclear DNA transfer. Human Genetics 112: 303–309; 2003.
Origin of the nucleus
Martin, W. A. briefly argued case that mitochondria and plastids are descendents of endosymbionts but that the nuclear compartment is not. Proceedings of the Royal Society of London B: Biological Sciences 266: 1387–1395; 1999.
Berry, S. Endosymbiosis and the design of eukaryotic electron transport. Biochimica et Biophysica Acta 1606: 57–72; 2003.
Fungi as the first eukaryotes
Martin, W., Rotte, C., Hoffmeister, M., Theissen, U., Gelius-Dietrich, G., Ahr, S., and Henze, K. Early cell evolution, eukaryotes, anoxia, sulfide, oxygen, fungi first (?), and a tree of genomes revisited. IUBMB (International Union of Biochemistry and Molecular Biology) Life 55: 193–204; 2003.
Why mitochondrial genes still exist
Allen, J. F. Control of gene expression by redox potential and the requirement for chloroplast and mitochondrial genes. Journal of Theoretical Biology 165: 609–631; 1993.
—— The function of genomes in bioenergetic organelles. Philosophical Transactions of the Royal Society of London B: Biological Sciences 358: 19–38; 2003.
—— Raven, J. A. Free-radical-induced mutation vs redox regulation: Costs and benefits of genes in organelles. Journal of Molecular Evolution 42: 482–492; 1996.
Chomyn, A. Mitochondrial genetic control of assembly and function of complex I in mammalian cells. Journal of Bioenergetics and Biomembranes 33: 251–257; 2001.
Race, H. L., Herrmann, R. G., and Martin, W. Why have organelles retained genomes? Trends in Genetics 15: 364–370; 1999.
Phylogeny of the ATP exporters
Andersson, S. G. E., Karlberg, O., Canbäck, B., and Kurland, C. G. On the origin of mitochondria: A genomics perspective. Philosophical Transactions of the Royal Society of London B: Biological Sciences 358: 165–179; 2003.
Löytynoja, A., and Milinkovitch, M. C. Molecular phylogenetic analyses of the mitochondrial ADP-ATP carriers: The plantae/fungi/metazoa trichotomy revisited. Proceedings of the National Academy of Sciences USA 98: 10202–10207; 2001.
Why bacteria are still bacteria
Lane, N. Mitochondria: Key to complexity. In W. Martin (ed.), Origins of Mitochondria and Hydrogenosomes. Springer, Heidelberg, Germany, 2006.
Part 4
General texts
Ball, Philip. The Self-Made Tapestry. Oxford University Press, Oxford, UK, 1999.
Gould, Stephen Jay. Full House. Random House, New York, USA, 1997.
Haldane, J. B. S. On Being the Right Size, ed. John Maynard-Smith. Oxford University Press, Oxford, UK, 1985.
Mandelbrot, Benoit. The Fractal Geometry of Nature. W. H. Freeman, New York, 1977.
Ridley, Mark. Mendel’s Demon. Weidenfeld & Nicolson, London, UK, 2000.
The power laws of biology
Bennett, A. F. Structural and functional determinates of metabolic rate. American Zoologist 28: 699–708; 1988.
Heusner, A. Size and power in mammals. Journal of Experimental Biology 160: 25–54; 1991.
Kleiber, M. The Fire of Life. Wiley, New York, USA, 1961.
Fractal geometry and scaling
Banavar, J., Damuth, J., Maritan, A., and Rinaldo, A. Supply-demand balance and metabolic scaling. Proceedings of the National Academy of Sciences USA 99: 10506–10509; 2002.
West, G. B., Brown J. H., and Enquist B. J. A general model for the origin of allometric scaling in biology. Science 276: 122–126; 1997.
—— —— —— The fourth dimension of life: Fractal geometry and allometric scaling of organisms. Science 284: 1677–1679; 1999.
—— Woodruff, W. H., and Brown, J. H. Allometric scaling of metabolic rate from molecules and mitochondria to cells and mammals. Proceedings of the National Academy of Sciences USA 99: 2473–2478; 2002.
Questioning the universal constant
Dodds, P. S., Rothman, D. H., and Weitz, J. S. Re-examination of the ‘3/4–law’ of metabolism. Journal of Theoretical Biology 209: 9–27; 2001.
White, C. R., and Seymour, R. S. Mammalian basal metabolic rate is proportional to body mass2/3. Proceedings of the National Academy of Sciences USA 100: 4046–4049; 2003.
Resting and maximal metabolic rates
Bishop, C. M. The maximum oxygen consumption and aerobic scope of birds and mammals: Getting to the heart of the matter. Proceedings of the Royal Society of London B: Biological Sciences 266: 2275–2281; 1999.
Tissue oxygen concentration in marine invertebrates and mammals
Massabuau, J. C. Primitive and protective, our cellular oxygenation status? Mechanisms of Ageing and Development 124: 857–863; 2003.
Components of metabolic rate in mammals
Porter, R. K. Allometry of mammalian cellular oxygen consumption. Cellular and Molecular Life Sciences 58: 815–822; 2001.
Rolfe, D. F. S., and Brown, G. C. Cellular energy utilization and molecular origin of standard metabolic rate in mammals. Physio
logical Reviews 77: 731–758; 1997.
Scaling of metabolic rate
Darveau, C. A., Suarez, R. K., Andrews, R. D., and Hochachka, P. W. Allometric cascade as a unifying principle of body mass effects on metabolism. Nature 417: 166–170; 2002.
Hochachka, P. W., Darveau, C. A., Andrews, R. D., and Suarez, R. K. Allometric cascade: A model for resolving body mass effects on metabolism. Comparative Biochemistry and Physiology A: Molecular and Integrative Physiology 134: 675–691; 2003.
Storey, K. B. Peter Hochachka and oxygen. In R. C. Roach et al. (eds.), Hypoxia: Through the Lifecycle. Kluwer Academic/Plenum Publishers, New York, USA, 2003.
Weibel, E. R. The pitfalls of power laws. Nature 417: 131–132; 2002.
Evolution of endothermy
Bennett, A. F., and Ruben, J. A. Endothermy and activity in vertebrates. Science 206:
649–653; 1979.
—— Hicks, J. W., and Cullum, A. J. An experimental test for the thermoregulatory hypothesis for the evolution of endothermy. Evolution 54: 1768–1773; 2000.
Hayes, J. P., and Garland, T., Jr. The evolution of endothermy: Testing the aerobic capacity hypothesis. Evolution 49: 836–847; 1995.
Ruben, J. The evolution of endothermy in mammals and birds: From physiology to fossils. Annual Review of Physiology 57: 69–85; 1995.
Mitochondria in muscles and organs of lizards and mammals
Else, P. L., and Hulbert, A. J. An allometric comparison of the mitochondria of mammalian and reptilian tissues: The implications for the evolution of endothermy. Journal of Comparative Physiology B: Biochemical, Systemic, and Environmental Physiology 156: 3–11; 1985.
Hulbert, A. J., and Else, P. L. Evolution of mammalian endothermic metabolism: Mitochondrial activity and cell composition. American Journal of Physiology 256: R63–R69; 1989.
Proton leak
Brand, M. D., Couture, P., Else, P. L., Withers, K. W., and Hulbert, A. J. Evolution of energy metabolism: Proton permeability of the inner membrane of liver mitochondria is greater in a mammal than in a reptile. Biochemical Journal 275: 81–86; 1991.
Brookes, P. S., Buckingham, J. A., Tenreiro, A. M., Hulbert, A. J., and Brand, M. D. The proton permeability of the inner membrane of liver mitochondria from ectothermic and endothermic vertebrates and from obese rats: Correlations with standard metabolic rate and phospholipid fatty acid composition. Comparative Biochemistry and Physiology 119B: 325–334; 1998.
Speakman, J. R., Talbot, D. A., Selman, C., Snart, S., McLaren, J. S., Redman, P., Krol, E., Jackson, D. M., Johnson, M. S., and Brand, M. D. Uncoupled and surviving: Individual mice with high metabolism have greater mitochondrial uncoupling and live longer. Aging Cell 3: 87–95; 2004.
Elastic strain in kangaroos
Bennett, M. B., and Taylor, G. C. Scaling of elastic strain energy in kangaroos and the benefits of being big. Nature 378: 56–59; 1995.
Cell volume, nuclear volume and DNA content
Cavalier-Smith, T. Economy, speed and size matter: Evolutionary forces driving nuclear genome miniaturization and expansion. Annals of Botany 95: 147–175; 2005.
Part 5
General texts
Buss, Leo. The Evolution of the Individual. Princeton University Press, New Jersey, USA, 1987.
Dawkins, Richard. The Selfish Gene. Oxford University Press, Oxford, UK, 1976.
Dawkins, Richard The Extended Phenotype. Oxford University Press, Oxford, UK, 1984.
—— The Ancestor’s Tale: A Pilgrimage to the Dawn of Life. Weidenfeld & Nicolson, London, UK, 2004.
Harold, Franklin. The Vital Force: A Study of Bioenergetics. W. H. Freeman and Co., New York, USA, 1986.
Klarsfeld, André, and Revah, Frédéric. The Biology of Death: Origins of Mortality. Cornell University Press, Ithaca, USA, 2004.
Margulis, Lynn. Gaia is a tough bitch. In John Brockman (ed.), The Third Culture: Beyond the Scientific Revolution. Simon & Schuster, New York, USA, 1995.
Maynard-Smith, John, and Szathmáry, Eörs. The Major Transitions of Evolution. W. H. Freeman, San Francisco, USA, 1995.
Levels of selection
Blackstone, N. W. A units-of-evolution perspective on the endosymbiont theory of the origin of the mitochondrion. Evolution 49: 785–796; 1995.
Maynard-Smith, J. The units of selection. Novartis Foundation Symposium 213: 203–211; 1998.
Mayr, E. The objects of selection. Proceedings of the National Academy of Sciences USA 94: 2091–2094; 1997.
Apoptosis and the evolution of multicellularity
Huettenbrenner, S., Maier, S., Leisser, C., Polgar, D., Strasser, S., Grusch, M., and Krupitza, G. The evolution of cell death programs as prerequisites of multicellularity. Mutation Research 543: 235–249; 2003.
Michod, R. E., and Roze, D. Cooperation and conflict in the evolution of multicellularity. Heredity 86: 1–7; 2001.
Discovery of apoptosis
Featherstone, C. Andrew Wyllie: From left field to centre stage. The Lancet 351: 192; 1998.
Kerr, J. F. History of the events leading to the formulation of the apoptosis concept. Toxicology 181–182: 471–474; 2002.
—— Wyllie A. H., and Currie A. R. Apoptosis: A basic biological phenomenon with wide-ranging implications in tissue kinetics. British Journal of Cancer 26: 239–257; 1972.
Caspase enzymes
Barinaga, M. Cell suicide: By ICE, not fire. Science 263: 754–756; 1994.
Horvitz, H. R. Nobel lecture: Worms, life and death. Bioscience Reports 23: 239–303; 2003.
—— Sulston, J. E. Joy of the worm. Genetics 126: 287–292; 1990.
Wiens, M., Krasko, A., Perovic, S., and Muller, W. E. G. Caspase-mediated apoptosis in sponges: cloning and function of the phylogenetic oldest apoptotic proteases from Metazoa. Biochimica et Biophysica Acta 1593: 179–189; 2003.
Mitochondrial involvement in apoptosis
Brown, G. C. Mitochondria and cell death. The Biochemist 27(3): 15–18; 2005.
Zamzami, N., Marchetti, P., Castedo, M., Zanin, C., Vayssière, J. L., Petit P. X., and Kroemer G. Reduction in mitochondrial potential constitutes an early irreversible step of programmed lymphocyte death in vivo. Journal of Experimental Medicine 181: 1661–1672; 1995.
—— —— —— Decaudin, D., Macho, A., Hirsch, T., Susin, S. A., Petit, P. X., Mignotte, B., and Kroemer, G. Sequential reduction of mitochondrial transmembrane potential and generation of reactive oxygen species in early programmed cell death. Journal of Experimental Medicine 182: 367–377; 1995.
—— Susin, S. A., Marchetti, P., Hirsch, T., Gómez-Monterret, I., Castedo, M., and Kroemer, G. Mitochondrial control of nuclear apoptosis. Journal of Experimental Medicine 183: 1533–1544; 1996.
Cytochrome c release
Balk, J., and Leaver, C. J. The PET-1–CMS mitochondrial mutation in sunflower is associated with premature programmed cell death and cytochrome c release. The Plant Cell 13: 1803–1818; 2001.
Kluck, R. M., Bossy-Wetzel, E., Green, D. R., and Newmeyer, D. D. The release of cytochrome c from mitochondria: A primary site for Bcl-2 regulation of apoptosis. Science 275: 1132–1136; 1997.
Liu, X., Kim, C. N., Yang, J., Jemmerson, R., and Wang, X. Induction of apoptotic program in cell-free extracts: Requirement for dATP and cytochrome c. Cell 86: 147–157; 1996.
Ott, M., Robertson, J. D., Gogvadze, V., Zhitotovsky, B., and Orrenius, S. Cytochrome c release from mitochondria proceeds by a two-step process. Proceedings of the National Academy of Sciences USA 99: 1259–1263; 2002.
Yang, J., Liu, X., Bhalla, K., Kim, C. N., Ibrado, A. M., Cai, J., Peng, T. I., Jones, D. P., and Wang, X. Prevention of apoptosis by Bcl-2: Release of cytochrome c from mitochondria blocked. Science 275: 1129–1132; 1997.
Other mitochondrial apoptotic proteins
Candé, C., Cecconi, F., Dessen, P., and Kroemer, G. Apoptosis-inducing factor (AIF) pathway: Key to the conserved caspase-independent pathways of cell death? Journal of Cell Science 115: 4727–4734; 2002.
van Gurp, M., Festjens, N.
, van Loo, G., Saelens, X., and Vandenabeele, P. Mitochondrial intermembrane proteins in cell death. Biochemical and Biophysical Research Communications 304: 487–497; 2003.
Bcl-2 family
Adams, J. M., and Cory, S. Life-or-death decisions by the Bcl-2 protein family. Trends in Biochemical Sciences 26: 61–66; 2001.