Книга: Вопрос жизни [Энергия, эволюция и происхождение сложности]
Библиография
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Библиография
Работы, на которые я ссылался здесь, сгруппированы по главам и темам внутри глав. Это не полный список. Я перечислил те книги и статьи, которые в последнее десятилетие в наибольшей степени повлияли на мой образ мышления. Я не всегда согласен с их авторами, но все они представляют интерес. Кроме того, в список для каждой главы я включил и собственные научные статьи. В них подробно обоснованы доводы, приведенные здесь в более общем виде. Там же вы найдете полный перечень процитированных работ.
Введение
Левенгук и начало микробиологии
Dobell, C. Antony van Leeuwenhoek and his Little Animals. Russell and Russell, New York (1958).
Kluyver, A. J. Three decades of progress in microbiology // Antonie van Leeuwenhoek 13: 1–20 (1947).
Lane, N. The unseen world: reflections on Leeuwenhoek (1677) “Concerning little animals” // Phil. Trans. R. Soc. B 370: 20140344 (2015).
Leewenhoeck, A. Observation, communicated to the publisher by Mr. Antony van Leewenhoeck, in a Dutch letter of the 9 Octob. 1676 here English’d: concerning little animals by him observed in rain-well-sea and snow water; as also in water wherein pepper had lain infused // Phil. Trans. R. Soc. B 12: 821–831 (1677).
Stanier, R. Y., and C. B. van Niel The concept of a bacterium // Archiv fur Microbiologie 42: 17–35 (1961).
Линн Маргулис и теория серийных эндосимбиозов
Archibald, J. One Plus One Equals One. Oxford University Press, Oxford (2014).
Margulis, L., Chapman, M., Guerrero, R., and J. Hall The last eukaryotic common ancestor (LECA): Acquisition of cytoskeletal motility from aerotolerant spirochetes in the Proterozoic Eon // Proceedings National Academy Sciences USA 103, 13080–13085 (2006).
Sagan, L. On the origin of mitosing cells // Journal of Theoretical Biology 14: 225–274 (1967).
Sapp, J. Evolution by Association: A History of Symbiosis. Oxford University Press, New York (1994).
Карл Везе и три домена жизни
Crick, F. H. C. The biological replication of macromolecules // Symposia of the Society of Experimental Biology 12, 138–163 (1958).
Morell, V. Microbiology’s scarred revolutionary // Science 276: 699–702 (1997).
Woese, C., Kandler, O., and M. L. Wheelis Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya // Proceedings National Academy Sciences USA 87: 4576–4579 (1990).
Woese, C. R., and G. E. Fox Phylogenetic structure of the prokaryotic domain: The primary kingdoms // Proceedings National Academy Sciences USA 74: 5088–5090 (1977).
Woese, C. R. A new biology for a new century // Microbiology and Molecular Biology Reviews 68: 173–186 (2004).
Билл Мартин и химерическое происхождение эукариот
Martin, W., and M. M?ller The hydrogen hypothesis for the first eukaryote // Nature 392: 37–41 (1998).
Martin, W. Mosaic bacterial chromosomes: a challenge en route to a tree of genomes // BioEssays 21: 99–104 (1999).
Pisani, D., Cotton, J. A., and J. O. McInerney Supertrees disentangle the chimeric origin of eukaryotic genomes // Molecular Biology and Evolution 24: 1752–1760 (2007).
Rivera, M. C., and J. A. Lake The ring of life provides evidence for a genome fusion origin of eukaryotes // Nature 431: 152–155 (2004).
Williams, T. A., Foster, P. G., Cox, C. J., and T. M. Embley An archaeal origin of eukaryotes supports only two primary domains of life // Nature 504: 231–236 (2013).
Питер Митчелл и хемиосмотическое сопряжение
Lane, N. Why are cells powered by proton gradients? // Nature Education 3: 18 (2010).
Mitchell, P. Coupling of phosphorylation to electron and hydrogen transfer by a chemiosmotic type of mechanism // Nature 191: 144–148 (1961).
Orgell, L. E. Are you serious, Dr Mitchell? // Nature 402: 17 (1999).
Глава 1. Что такое жизнь?
Вероятность возникновения жизни и ее свойства
Conway-Morris, S. J. Life’s Solution: Inevitable Humans in a Lonely Universe. Cambridge University Press, Cambridge (2003).
Duve, C. de Life Evolving: Molecules, Mind, and Meaning. Oxford University Press, Oxford (2002).
Duve, C. de Singularities: Landmarks on the Pathways of Life. Cambridge University Press, Cambridge (2005).
Gould, S. J. Wonderful Life. The Burgess Shale and the Nature of History. W. W. Norton, New York (1989).
Maynard Smith, J., and E. Szathm?ry The Major Transitions in Evolution. Oxford University Press, Oxford (1995).
Monod, J. Chance and Necessity. Alfred A. Knopf, New York (1971).
Основы молекулярной биологии
Cobb, M. 1953: When genes became information // Cell 153: 503–506 (2013).
Cobb, M. Life’s Greatest Secret: The Story of the Race to Crack the Genetic Code. Profile, London (2015).
Schr?dinger, E. What is Life? Cambridge University Press, Cambridge (1944).
Watson, J. D., and F. H. C. Crick Genetical implications of the structure of deoxyribonucleic acid // Nature 171: 964–967 (1953).
Размер и структура генома
Doolittle, W. F. Is junk DNA bunk? A critique of ENCODE // Proceedings National Academy Sciences USA 110: 5294–5300 (2013).
Grauer, D., Zheng, Y., Price, N., Azevedo, R. B. R., Zufall, R. A., and E. Elhaik On the immortality of television sets: “functions” in the human genome according to the evolution-free gospel of ENCODE // Genome Biology and Evolution 5: 578–590 (2013).
Gregory, T. R. Synergy between sequence and size in large-scale genomics // Nature Reviews Genetics 6: 699–708 (2005).
Первые два миллиарда лет жизни на Земле
Arndt, N., and E. Nisbet Processes on the young Еarth and the habitats of early life // Annual Reviews Earth and Planetary Sciences 40: 521–549 (2012).
Hazen, R. The Story of Earth: The First 4,5 Billion Years, from Stardust to Living Planet. Viking, New York (2014).
Knoll, A. Life on a Young Planet: The First Three Billion Years of Evolution on Earth. Princeton University Press, Princeton (2003).
Rutherford, A. Creation: The Origin of Life / The Future of Life. Viking Press, London (2013).
Zahnle, K., Arndt, N., Cockell, C., Halliday, A., Nisbet, E., Selsis, F., and N. H. Sleep Emergence of a habitable planet // Space Science Reviews 129: 35–78 (2007).
Появление кислорода
Butterfield, N. J. Oxygen, animals and oceanic ventilation: an alternative view // Geobiology 7: 1–7 (2009).
Canfield, D. E. Oxygen: A Four Billion Year History. Princeton University Press, Princeton (2014).
Catling, D. C., Glein, C. R., Zahnle, K. J., and C. P. Mckay Why O2is required by complex life on habitable planets and the concept of planetary “oxygenation time” // Astrobiology 5: 415–438 (2005).
Holland, H. D. The oxygenation of the atmosphere and oceans // Phil. Trans. R. Soc. B 361: 903–915 (2006).
Lane, N. Life’s a gas // New Scientist 2746: 36–39 (2010).
Lane, N. Oxygen: The Molecule that Made the World. Oxford University Press, Oxford (2002).
Shields-Zhou, G., and L. Och The case for a Neoproterozoic oxygenation event: Geochemical evidence and biological consequences // GSA Today 21: 4–11 (2011).
Предположения на основе гипотезы серийных эндосимбиозов
Archibald, J. M. Origin of eukaryotic cells: 40 years on // Symbiosis 54: 69–86 (2011).
Margulis, L. Genetic and evolutionary consequences of symbiosis // Experimental Parasitology 39: 277–349 (1976).
O’Malley, M. The first eukaryote cell: an unfinished history of contestation // Studies in History and Philosophy of Biological and Biomedical Sciences 41: 212–224 (2010).
Архезои
Cavalier-Smith, T. Archaebacteria and archezoa // Nature 339: 100–101 (1989).
Cavalier-Smith, T. Predation and eukaryotic origins: A coevolutionary perspective // International Journal of Biochemistry and Cell Biology 41: 307–332 (2009).
Giezen, M. van der Hydrogenosomes and mitosomes: Conservation and evolution of functions // Journal of Eukaryotic Microbiology 56: 221–231 (2009).
Henze, K., and W. Martin Essence of mitochondria // Nature 426: 127–128 (2003).
Martin, W. F., and M. M?ller Origin of Mitochondria and Hydrogenosomes. Springer, Heidelberg (2007).
Tielens, A. G. M., Rotte, C., Hellemond, J. J., and W. Martin Mitochondria as we don’t know them // Trends in Biochemical Sciences 27: 564–572 (2002).
Yong, E. The unique merger that made you (and ewe and yew) // Nautilus 17: Sept 4 (2014).
Супергруппы эукариот
Baldauf, S. L., Roger, A. J., Wenk-Siefert, I., and W. F. Doolittle A kingdom-level phylogeny of eukaryotes based on combined protein data // Science 290: 972–977 (2000).
Hampl, V., Huga, L., Leigh, J. W., Dacks, J. B., Lang, B. F., Simpson, A. G. B., and A. J. Roger Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups” // Proceedings National Academy Sciences USA 106: 3859–3864 (2009).
Keeling, P. J., Burger, G., Durnford, D. G., Lang, B. F., Lee, R. W., Pearlman, R. E., Roger, A. J., and M. W. Grey The Tree of eukaryotes // Trends in Ecology and Evolution 20: 670–676 (2005).
Последний общий предок эукариот
Embley T. M., and W. Martin Eukaryotic evolution, changes and challenges // Nature 440: 623–630 (2006).
Harold, F. In Search of Cell History: The Evolution of Life’s Building Blocks. Chicago University Press, Chicago (2014).
Koonin, E. V. The origin and early evolution of eukaryotes in the light of phylogenomics // Genome Biology 11: 209 (2010).
McInerney, J. O., Martin, W. F., Koonin, E. V., Allen, J. F., Galperin, M. Y., Lane, N., Archibald, J. M., and T. M. Embley Planctomycetes and eukaryotes: a case of analogy not homology // BioEssays 33: 810–817 (2011).
Парадокс малых шагов к сложности
Darwin, C. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. 1st edn. John Murray, London (1859).
Land, M. F., and D.-E. Nilsson Animal Eyes. Oxford University Press, Oxford (2002).
Lane, N. Bioenergetic constraints on the evolution of complex life // Cold Spring Harbor Perspectives in Biology, doi: 10.1101/cshperspect.a015982 (2014).
Lane, N. Energetics and genetics across the prokaryote-eukaryote divide // Biology Direct 6: 35 (2011).
M?ller, M., Mentel, M., van Hellemond, J. J., Henze, K., Woehle, C., Gould, S. B., Yu, R. Y., van der Giezen, M., Tielens, A. G., and W. F. Martin Biochemistry and evolution of anaerobic energy metabolism in eukaryotes // Microbiology and Molecular Biology Reviews 76: 444–495 (2012).
Глава 2. Что значит жить?
Энергия, энтропия и структура
Amend, J. P., LaRowe, D. E., McCollom, T. M., and E. L. Shock The energetics of organic synthesis inside and outside the cell // Phil. Trans. R. Soc. B. 368: 20120255 (2013).
Battley, E. H. Energetics of Microbial Growth. Wiley Interscience, New York (1987).
Hansen L. D., Criddle, R. S., and E. H. Battley Biological calorimetry and the thermodynamics of the origination and evolution of life // Pure and Applied Chemistry 81: 1843–1855 (2009).
McCollom, T., and J. P. Amend A thermodynamic assessment of energy requirements for biomass synthesis by chemolithoautotrophic micro-organisms in oxic and micro-oxic environments // Geobiology 3: 135–144 (2005).
Minsky, A., Shimoni, E., and D. Frenkiel-Krispin Stress, order and survival // Nature Reviews in Molecular Cell Biology 3: 50–60 (2002).
Скорость синтеза АТФ
Fenchel, T., and B. J. Finlay Respiration rates in heterotrophic, free-living protozoa // Microbial Ecology 9: 99–122 (1983).
Makarieva, A. M., Gorshkov, V. G., and B. L. Li Energetics of the smallest: do bacteria breathe at the same rate as whales? Proc. R. Soc. B 272: 2219–2224 (2005).
Phillips, R., Kondev, J., Theriot, J., and H. Garcia Physical Biology of the Cell. Garland Science, New York (2012).
Rich, P. R. The cost of living // Nature 421: 583 (2003).
Schatz, G. The tragic matter // FEBS Letters 536: 1–2 (2003).
Механизм дыхания и синтез АТФ
Abrahams, J. P., Leslie, A. G., Lutter, R., and J. E. Walker Structure at 2.8 A resolution of F1-ATPase from bovine heart mitochondria // Nature 370: 621–628 (1994).
Baradaran, R., Berrisford, J. M., Minhas, S. G., and L. A. Sazanov Crystal structure of the entire respiratory complex I // Nature 494: 443–448 (2013).
Hayashi, T., and A. A. Stuchebrukhov Quantum electron tunneling in respiratory complex I // Journal of Physical Chemistry B 115: 5354–5364 (2011).
Moser, C. C., Page, C. C., and P. L. Dutton Darwin at the molecular scale: selection and variance in electron tunnelling proteins including cytochrome c oxidase // Phil. Trans. R. Soc. B 361: 1295–1305 (2006).
Murata, T., Yamato, I., Kakinuma, Y., Leslie, A. G. W., and J. E. Walker Structure of the rotor of the V-type Na+-ATPase from Enterococcus hirae // Science 308: 654–659 (2005).
Nicholls, D. G., and S. J. Ferguson Bioenergetics. 4th edn. Academic Press, London (2013).
Stewart, A. G., Sobti, M., Harvey, R. P., and D. Stock Rotary ATPases: Models, machine elements and technical specifications // BioArchitecture 3: 2–12 (2013).
Vinothkumar, K. R., Zhu, J., and J. Hirst Architecture of the mammalian respiratory complex I // Nature 515: 80–84 (2014).
Питер Митчелл и хемиосмотическое сопряжение
Harold, F. M. The Way of the Cell: Molecules, Organisms, and the Order of Life. Oxford University Press, New York (2003).
Lane, N. Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press, Oxford (2005).
Mitchell, P. Coupling of phosphorylation to electron and hydrogen transfer by a chemiosmotic type of mechanism // Nature 191: 144–148 (1961).
Mitchell, P. Keilin’s respiratory chain concept and its chemiosmotic consequences // Science 206: 1148–1159 (1979).
Mitchell, P. The origin of life and the formation and organising functions of natural membranes / In: Proceedings of the first international symposium on the origin of life on the Earth. Oparin, A. I., Pasynski, A. G., Braunstein, A. E., and T. E. Pavlovskaya, eds. Moscow Academy of Sciences, USSR (1957).
Prebble, J., and B. Weber Wandering in the Gardens of the Mind. Oxford University Press, New York (2003).
Углерод и необходимость окислительно-восстановительных реакций
Falkowski, P. Life’s engines: how microbes made Еarth habitable. Princeton University Press, Princeton (2015).
Kim, J. D., Senn, S., Harel, A., Jelen, B. I., and P. G. Falkowski Discovering the electronic circuit diagram of life: structural relationships among transition metal binding sites in oxidoreductases // Phil. Trans. R. Soc. B 368: 20120257 (2013).
Morton, O. Eating the Sun: How Plants Power the Planet. Fourth Estate, London (2007).
Pace, N. The universal nature of biochemistry // Proceedings National Academy Sciences USA 98: 805–808 (2001).
Schoepp-Cothenet, B., van Lis, R., Atteia, A., Baymann, F., Capowiez, L., Ducluzeau, A.-L., Duval, S., Brink, F. ten, Russell, M. J., and W. Nitschke On the universal core of bioenergetics // Biochimica Biophysica Acta Bioenergetics 1827: 79–93 (2013).
Фундаментальные различия бактерий и архей
Edgell, D. R., and W. F. Doolittle Archaea and the origin(s) of DNA replication proteins // Cell 89: 995–998 (1997).
Koga, Y., Kyuragi, T., Nishihara, M., and N. Sone Did archaeal and bacterial cells arise independently from noncellular precursors? A hypothesis stating that the advent of membrane phospholipid with enantiomeric glycerophosphate backbones caused the separation of the two lines of descent // Journal of Molecular Evolution 46: 54–63 (1998).
Leipe, D. D., Aravind, L., and E. V. Koonin Did DNA replication evolve twice independently? // Nucleic Acids Research 27: 3389–3401 (1999).
Lombard, J., L?pez-Garc?a, P., and D. Moreira The early evolution of lipid membranes and the three domains of life // Nature Reviews Microbiology 10: 507–515 (2012).
Martin, W., and M. J. Russell On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells // Phil. Trans. R. Soc. B 358: 59–83 (2003).
Sousa, F. L., Thiergart, T., Landan, G., Nelson-Sathi, S., Pereira, I. A. C., Allen, J. F., Lane, N., and W. F. Martin Early bioenergetic evolution // Phil. Trans. R. Soc. B 368: 20130088 (2013).
Глава 3. Энергия и начало жизни
Энергетические потребности на заре жизни
Lane, N., Allen, J. F., and W. Martin How did LUCA make a living? Chemiosmosis in the origin of life // BioEssays 32: 271–280 (2010).
Lane, N., and W. Martin The origin of membrane bioenergetics // Cell 151: 1406–1416 (2012).
Martin, W., Sousa, F. L., and N. Lane Energy at life’s origin // Science 344: 1092–1093 (2014).
Martin, W. F. Hydrogen, metals, bifurcating electrons, and proton gradients: The early evolution of biological energy conservation // FEBS Letters 586: 485–493 (2012).
Russell, M., ed. Origins: Abiogenesis and the Search for Life. Cosmology Science Publishers, Cambridge MA (2011).
Эксперимент Миллера – Юри и “мир РНК”
Joyce, G. F. RNA evolution and the origins of life // Nature 33: 217–224 (1989).
Miller, S. L. A production of amino acids under possible primitive Earth conditions // Science 117: 528–529 (1953).
Orgel, L. E. Prebiotic chemistry and the origin of the RNA world // Critical Reviews in Biochemistry and Molecular Biology 39: 99–123 (2004).
Powner, M. W., Gerland, B., and J. D. Sutherland Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions // Nature 459: 239–242 (2009).
Термодинамика далеких от равновесия процессов
Morowitz, H. Energy Flow in Biology: Biological Organization as a Problem in Thermal Physics. Academic Press, New York (1968).
Prigogine, I. The End of Certainty: Time, Chaos and the New Laws of Nature. Free Press, New York (1997).
Russell, M. J., Nitschke, W., and E. Branscomb The inevitable journey to being // Phil. Trans. R. Soc. B 368: 20120254 (2013).
Происхождение катализа
Cody, G. Transition metal sulfides and the origins of metabolism // Annual Review Earth and Planetary Sciences 32: 569–599 (2004).
Russell, M. J., Allen, J. F., and E. J. Milner-White Inorganic complexes enabled the onset of life and oxygenic photosynthesis / In: Allen, J. F., Gantt, E., Golbeck, J. H., and B. Osmond Energy from the Sun: 14th International Congress on Photosynthesis. Springer, Heidelberg (2008).
Russell, M. J., and W. Martin The rocky roots of the acetyl-CoA pathway // Trends in Biochemical Sciences 29: 358–363 (2004).
Реакции дегидратации в воде
Benner, S. A., Kim, H.-J., and M. A. Carrigan Asphalt, water, and the prebiotic synthesis of ribose, ribonucleosides, and RNA // Accounts of Chemical Research 45: 2025–2034 (2012).
Pratt, A. J. Prebiological evolution and the metabolic origins of life // Artificial Life 17: 203–217 (2011).
Zwart, I. I. de, Meade, S. J., and A. J. Pratt Biomimetic phosphoryl transfer catalysed by iron(II) – mineral precipitates // Geochimica et Cosmochimica Acta 68: 4093–4098 (2004).
Формирование протоклеток
Budin, I., Bruckner, R. J., and J. W. Szostak Formation of protocell-like vesicles in a thermal diffusion column // Journal of the American Chemical Society 131: 9628–9629 (2009).
Errington, J. L-form bacteria, cell walls and the origins of life // Open Biology 3: 120143 (2013).
Hanczyc, M., Fujikawa, S., and J. Szostak Experimental models of primitive cellular compartments: encapsulation, growth, and division // Science 302: 618–622 (2003).
Mauer, S. E., and P. A. Monndard Primitive membrane formation, characteristics and roles in the emergent properties of a protocell // Entropy 13: 466–484 (2011).
Szathm?ry, E., Santos, M., and C. Fernando Evolutionary potential and requirements for minimal protocells // Topics in Current Chemistry 259: 167–211 (2005).
Возникновение репликации
Cairns-Smith, G. Seven Clues to the Origin of Life. Cambridge University Press, Cambridge (1990).
Costanzo, G., Pino, S., Ciciriello, F., and E. Di Mauro Generation of long RNA chains in water // Journal of Biological Chemistry 284: 33206–33216 (2009).
Koonin, E. V., and W. Martin On the origin of genomes and cells within inorganic compartments // Trends in Genetics 21: 647–654 (2005).
Mast, C. B., Schink, S., Gerland, U., and D. Braun Escalation of polymerization in a thermal gradient // Proceedings of the National Academy of Sciences USA 110: 8030–8035 (2013).
Mills, D. R., Peterson, R. L., and S. Spiegelman An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule // Proceedings National Academy Sciences USA 58: 217–224 (1967).
Открытие глубоководных гидротермальных источников
Baross, J. A., and S. E. Hoffman Submarine hydrothermal vents and associated gradient environments as sites for the origin and evolution of life // Origins Life Evolution of the Biosphere 15: 327–345 (1985).
Kelley, D. S., Karson, J. A., Blackman, D. K., et al. An off-axis hydrothermal vent field near the Mid-Atlantic Ridge at 30 degrees N. // Nature 412: 145–149 (2001).
Kelley, D. S., Karson, J. A., Fr?h-Green, G. L., et al. A serpentinite-hosted submarine ecosystem: the Lost City Hydrothermal Field // Science 307: 1428–1434 (2005).
Пиритный пуллинг и железосерный мир
Duve, C. de, and S. Miller Two-dimensional life? // Proceedings National Academy Sciences USA 88: 10014–10017 (1991).
Huber, C., and G. W?ctersh?user Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions // Science 276: 245–247 (1997).
Miller, S. L., and J. L. Bada Submarine hot springs and the origin of life // Nature 334: 609–611 (1988).
W?ctersh?user, G. Evolution of the first metabolic cycles // Proceedings National Academy Sciences USA 87: 200–204 (1990).
W?ctersh?user, G. From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya // Phil. Trans. R. Soc. B 361: 1787–1806 (2006).
Щелочные гидротермальные источники
Martin, W., Baross, J., Kelley, D., and M. J. Russell Hydrothermal vents and the origin of life // Nature Reviews Microbiology 6: 805–814 (2008).
Martin, W., and M. J. Russell On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells // Phil. Trans. R. Soc. B 358: 59–83 (2003).
Russell, M. J., Daniel, R. M., Hall, A. J., and J. Sherringham A hydrothermally precipitated catalytic iron sulphide membrane as a first step toward life // Journal of Molecular Evolution 39: 231–243 (1994).
Russell, M. J., Hall, A. J., Cairns-Smith, A. G., and P. S. Braterman Submarine hot springs and the origin of life // Nature 336: 117 (1988).
Russell, M. J., and A. J. Hall The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front // Journal Geological Society London 154: 377–402 (1997).
Серпентинизация
Fyfe, W. S. The water inventory of the Earth: fluids and tectonics // Geological Society of London Special Publications 78: 1–7 (1994).
Russell, M. J., Hall, A. J., and W. Martin Serpentinization as a source of energy at the origin of life // Geobiology 8: 355–371 (2010).
Sleep, N. H., Bird, D. K., and E. C. Pope Serpentinite and the dawn of life // Phil. Trans. R. Soc. B 366: 2857–2869 (2011).
Химия катархейских океанов
Arndt, N., and E. Nisbet Processes on the young Earth and the habitats of early life // Annual Reviews Earth Planetary Sciences 40: 521–549 (2012).
Pinti, D. The origin and evolution of the oceans // Lectures Astrobiology 1: 83–112 (2005).
Russell, M. J., and N. T. Arndt Geodynamic and metabolic cycles in the Hadean // Biogeosciences 2: 97–111 (2005).
Zahnle, K., Arndt, N., Cockell, C., Halliday, A., Nisbet, E., Selsis, F., and N. H. Sleep Emergence of a habitable planet // Space Science Reviews 129: 35–78 (2007).
Термофорез
Baaske, P., Weinert, F. M., Duhr, S., et al. Extreme accumulation of nucleotides in simulated hydrothermal pore systems // Proceedings National Academy Sciences USA 104: 9346–9351 (2007).
Mast, C. B., Schink, S., Gerland, U., and D. Braun Escalation of polymerization in a thermal gradient // Proceedings National Academy Sciences USA 110: 8030–8035 (2013).
Термодинамика синтеза органических веществ в щелочных источниках
Amend, J. P., and T. M. McCollom Energetics of biomolecule synthesis on early Earth / In: Zaikowski, L., et al., eds. Chemical Evolution II: From the Origins of Life to Modern Society. American Chemical Society (2009).
Ducluzeau, A.-L., Schoepp-Cothenet, B., Baymann, F., Russell, M. J., and W. Nitschke Free energy conversion in the LUCA: Quo vadis? // Biochimica et Biophysica Acta Bioenergetics 1837: 982–988 (2014).
Martin, W., and M. J. Russell On the origin of biochemistry at an alkaline hydrothermal vent // Phil. Trans. R. Soc. B 367: 1887–1925 (2007).
Shock, E., and P. Canovas The potential for abiotic organic synthesis and biosynthesis at seafloor hydrothermal systems // Geofluids 10: 161–192 (2010).
Sousa, F. L., Thiergart, T., Landan, G., Nelson-Sathi, S., Pereira, I. A. C., Allen, J. F., Lane, N., and W. F. Martin Early bioenergetic evolution // Phil. Trans. R. Soc. B 368: 20130088 (2013).
Восстановительный потенциал и кинетический барьер восстановления CO2
Lane, N., and W. Martin The origin of membrane bioenergetics // Cell 151: 1406–1416 (2012).
Maden, B. E. H. Tetrahydrofolate and tetrahydromethanopterin compared: functionally distinct carriers in C1metabolism // Biochemical Journal 350: 609–629 (2000).
W?ctersh?user, G. Pyrite formation, the ?rst energy source for life: a hypothesis // Systematic and Applied Microbiology 10: 207–210 (1988).
Могут ли природные протонные градиенты инициировать восстановление CO2?
Herschy, B., Whicher, A., Camprubi, E., Watson, C., Dartnell, L., Ward, J., Evans, J. R. G., and N. Lane An origin-of-life reactor to simulate alkaline hydrothermal vents // Journal of Molecular Evolution 79: 213–227 (2014).
Herschy, B. Nature’s electrochemical flow reactors: Alkaline hydrothermal vents and the origins of life // Biochemist 36: 4–8 (2014).
Lane, N. Bioenergetic constraints on the evolution of complex life // Cold Spring Harbor Perspectives in Biology, doi: 10.1101/cshperspect.a015982 (2014).
Nitschke, W., and M. J. Russell Hydrothermal focusing of chemical and chemiosmotic energy, supported by delivery of catalytic Fe, Ni, Mo, Co, S and Se forced life to emerge // Journal of Molecular Evolution 69: 481–496 (2009).
Yamaguchi, A., Yamamoto, M., Takai, K., Ishii, T., Hashimoto, K., and R. Nakamura Electrochemical CO2reduction by Nicontaining iron sulfides: how is CO2electrochemically reduced at bisulfide-bearing deep sea hydrothermal precipitates? // Electrochimica Acta 141: 311–318 (2014).
Вероятность серпентинизации на других планетах Млечного Пути
Leeuw, N. H. de, Catlow, C. R., King, H. E., Putnis, A., Muralidharan, K., Deymier, P., Stimpfl, M., and M. J. Drake Where on Earth has our water come from? // Chemical Communications 46: 8923–8925 (2010).
Petigura, E. A., Howard, A. W., and G. W. Marcy Prevalence of Earth-sized planets orbiting Sunlike stars // Proceedings National Academy Sciences USA 110: 19273–19278 (2013).
Глава 4. Появление первых клеток
Горизонтальный перенос генов и видообразование
Doolittle, W. F. Phylogenetic classification and the universal tree // Science 284: 2124–2128 (1999).
Lawton, G. Why Darwin was wrong about the tree of life // New Scientist 2692: 34–39 (2009).
Mallet, J. Why was Darwin’s view of species rejected by twentieth century biologists? // Biology and Philosophy 25: 497–527 (2010).
Martin, W. F. Early evolution without a tree of life // Biology Direct 6: 36 (2011).
Nelson-Sathi, S., et al. Origins of major archaeal clades correspond to gene acquisitions from bacteria // Nature, doi: 10.1038/nature13805 (2014).
“Единое дерево жизни”, построенное менее чем по 1 % генов
Ciccarelli, F. D., Doerks, T., Mering, C. von, Creevey, C. J., Snel, B., et al. Toward automatic reconstruction of a highly resolved tree of life // Science 311: 1283–1287 (2006).
Dagan, T., and W. Martin The tree of one percent // Genome Biology 7: 118 (2006).
Гены архей и бактерий
Charlebois, R. L., and W. F. Doolittle Computing prokaryotic gene ubiquity: Rescuing the core from extinction // Genome Research 14: 2469–2477 (2004).
Koonin, E. V. Comparative genomics, minimal gene-sets and the last universal common ancestor // Nature Reviews Microbiology 1: 127–136 (2003).
Sousa, F. L., Thiergart, T., Landan, G., Nelson-Sathi, S., Pereira, I. A. C., Allen, J. F., Lane, N., and W. F. Martin Early bioenergetic evolution // Phil. Trans. R. Soc. B 368: 20130088 (2013).
Последний всеобщий предок
Dagan, T., and W. Martin Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution // Proceedings National Academy Sciences USA 104: 870–875 (2007).
Edgell, D. R., and W. F. Doolittle Archaea and the origin(s) of DNA replication proteins // Cell 89: 995–998 (1997).
Koga, Y., Kyuragi, T., Nishihara, M., and N. Sone Did archaeal and bacterial cells arise independently from noncellular precursors? A hypothesis stating that the advent of membrane phospholipid with enantiomeric glycerophosphate backbones caused the separation of the two lines of descent // Journal of Molecular Evolution 46: 54–63 (1998).
Leipe, D. D., Aravind, L., and E. V. Koonin Did DNA replication evolve twice independently? // Nucleic Acids Research 27: 3389–3401 (1999).
Martin, W., and M. J. Russell On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells // Phil. Trans. R. Soc. B 358: 59–83 (2003).
Проблема мембранных липидов
Lane, N., and W. Martin The origin of membrane bioenergetics // Cell 151: 1406–1416 (2012).
Lombard, J., L?pez-Garc?a, P., and D. Moreira The early evolution of lipid membranes and the three domains of life // Nature Reviews in Microbiology 10: 507–515 (2012).
Shimada, H., and A. Yamagishi Stability of heterochiral hybrid membrane made of bacterial sn-G3P lipids and archaeal sn-G1P lipids // Biochemistry 50: 4114–4120 (2011).
Valentine, D. Adaptations to energy stress dictate the ecology and evolution of the Archaea // Nature Reviews Microbiology 5: 1070–1077 (2007).
Путь Вуда – Льюнгдаля
Fuchs, G. Alternative pathways of carbon dioxide fixation: Insights into the early evolution of life? // Annual Review Microbiology 65: 631–658 (2011).
Ljungdahl, L. G. A life with acetogens, thermophiles, and cellulolytic anaerobes // Annual Review Microbiology 63: 1–25 (2009).
Maden, B. E. H. No soup for starters? Autotrophy and the origins of metabolism // Trends in Biochemical Sciences 20: 337–341 (1995).
Ragsdale, S. W., and E. Pierce Acetogenesis and the Wood – Ljungdahl pathway of CO2fixation // Biochimica Biophysica Acta 1784: 1873–1898 (2008).
Геологические основы пути Вуда – Льюнгдаля
Nitschke, W., McGlynn, S. E., Milner-White, J., and M. J. Russell On the antiquity of metalloenzymes and their substrates in bioenergetics // Biochimica Biophysica Acta 1827: 871–881 (2013).
Russell, M. J., and W. Martin The rocky roots of the acetyl-CoA pathway // Trends in Biochemical Sciences 29: 358–363 (2004).
Абиотический синтез ацетилтиоэфиров и ацетилфосфата
Duve, C. de Did God make RNA? // Nature 336: 209–210 (1988).
Heinen, W., and A. M. Lauwers Sulfur compounds resulting from the interaction of iron sulfide, hydrogen sulfide and carbon dioxide in an anaerobic aqueous environment // Origins Life Evolution Biosphere 26: 131–150 (1996).
Huber, C., and G. W?ctersh?user Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions // Science 276: 245–247 (1997).
Martin, W., and M. J. Russell On the origin of biochemistry at an alkaline hydrothermal vent // Phil. Trans. R. Soc. B 367: 1887–1925 (2007).
Возможное происхождение генетического кода
Copley, S. D., Smith, E., and H. J. Morowitz A mechanism for the association of amino acids with their codons and the origin of the genetic code // Proceedings National Academy Sciences USA 102: 4442–4447 (2005).
Lane, N. Life Ascending: The Ten Great Inventions of Evolution. W. W. Norton/Profile, London (2009).
Taylor, F. J., and D. Coates The code within the codons // Biosystems 22: 177–187 (1989).
Сходство между условиями щелочных гидротермальных источников и путем Вуда – Льюнгдаля
Herschy, B., Whicher, A., Camprubi, E., Watson, C., Dartnell, L., Ward, J., Evans, J. R. G., and N. Lane An origin-of-life reactor to simulate alkaline hydrothermal vents // Journal of Molecular Evolution 79: 213–227 (2014).
Lane, N. Bioenergetic constraints on the evolution of complex life // Cold Spring Harbor Perspectives in Biology, doi: 10.1101/cshperspect.a015982 (2014).
Martin, W., Sousa, F. L., and N. Lane Energy at life’s origin // Science 344: 1092–1093 (2014).
Sousa, F. L., Thiergart, T., Landan, G., Nelson-Sathi, S., Pereira, I. A. C., Allen, J. F., Lane, N., and W. F. Martin Early bioenergetic evolution // Phil. Trans. R. Soc. B 368: 20130088 (2013).
Проблема мембранной проницаемости
Lane, N., and W. Martin The origin of membrane bioenergetics // Cell 151: 1406–1416 (2012).
Le Page, M. Meet your maker // New Scientist 2982: 30–33 (2014).
Mulkidjanian, A. Y., Bychkov, A. Y., Dibrova, D. V., Galperin, M. Y., and E. V. Koonin Origin of first cells at terrestrial, anoxic geothermal fields // Proceedings National Academy Sciences USA 109: E821-E830 (2012).
Sojo, V., Pomiankowski, A., and N. Lane A bioenergetic basis for membrane divergence in archaea and bacteria // PLoS Biology 12 (8): e1001926 (2014).
Yong, E. How life emerged from deep-sea rocks // Nature, doi: 10.1038/nature.2012.12109 (2012).
Мембранные белки не делают различий между H+и Na+
Buckel, W., and R. K. Thauer Energy conservation via electron bifurcating ferredoxin reduction and proton/Na(+) translocating ferredoxin oxidation // Biochimica Biophysica Acta 1827: 94–113 (2013).
Lane, N., Allen, J. F., and W. Martin How did LUCA make a living? Chemiosmosis in the origin of life // BioEssays 32: 271–280 (2010).
Schlegel, K., Leone, V., Faraldo-G?mez, J. D., and V. M?ller Promiscuous archaeal ATP synthase concurrently coupled to Na+and H+translocation // Proceedings National Academy Sciences USA 109: 947–952 (2012).
Бифуркация электронов
Buckel, W., and R. K. Thauer Energy conservation via electron bifurcating ferredoxin reduction and proton/Na(+) translocating ferredoxin oxidation // Biochimica Biophysica Acta 1827: 94–113 (2013).
Kaster, A.-K., Moll, J., Parey, K., and R. K. Thauer Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic Archaea // Proceedings National Academy Sciences USA 108: 2981–2986 (2011).
Thauer, R. K. A novel mechanism of energetic coupling in anaerobes // Environmental Microbiology Reports 3: 24–25 (2011).
Глава 5. Появление сложных клеток
Размеры геномов
Cavalier-Smith, T. Economy, speed and size matter: evolutionary forces driving nuclear genome miniaturization and expansion // Annals of Botany 95: 147–175 (2005).
Cavalier-Smith, T. Skeletal DNA and the evolution of genome size // Annual Review of Biophysics and Bioengineering 11: 273–301 (1982).
Gregory, T. R. Synergy between sequence and size in large-scale genomics // Nature Reviews in Genetics 6: 699–708 (2005).
Lynch, M. The Origins of Genome Architecture. Sinauer Associates, Sunderland MA (2007).
Возможные ограничения размера генома у эукариот
Cavalier-Smith, T. Predation and eukaryote cell origins: A coevolutionary perspective // International Journal Biochemistry Cell Biology 41: 307–322 (2009).
Duve, C. de The origin of eukaryotes: a reappraisal // Nature Reviews in Genetics 8: 395–403 (2007).
Koonin, E. V. Evolution of genome architecture // International Journal Biochemistry Cell Biology 41: 298–306 (2009).
Lynch, M., and J. S. Conery The origins of genome complexity // Science 302: 1401–1404 (2003).
Maynard Smith, J., and E. Szathm?ry The Major Transitions in Evolution. Oxford University Press, Oxford. (1995).
Химерное происхождение эукариот
Cotton, J. A., and J. O. McInerney Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function // Proceedings National Academy Sciences USA 107: 17252–17255 (2010).
Esser, C., Ahmadinejad, N., Wiegand, C., et al. A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes // Molecular Biology Evolution 21: 1643–1660 (2004).
Koonin, E. V. Darwinian evolution in the light of genomics // Nucleic Acids Research 37: 1011–1034 (2009).
Pisani, D., Cotton, J. A., and J. O. McInerney Supertrees disentangle the chimeric origin of eukaryotic genomes // Molecular Biology Evolution 24: 1752–1760 (2007).
Rivera, M. C., and J. A. Lake The ring of life provides evidence for a genome fusion origin of eukaryotes // Nature 431: 152–155 (2004).
Thiergart, T., Landan, G., Schrenk, M., Dagan, T., and W. F. Martin An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin // Genome Biology and Evolution 4: 466–485 (2012).
Williams, T. A., Foster, P. G., Cox, C. J., and T. M. Embley An archaeal origin of eukaryotes supports only two primary domains of life // Nature 504: 231–236 (2013).
Позднее происхождение брожения
Say, R. F., and G. Fuchs Fructose 1,6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme // Nature 464: 1077–1081 (2010).
Стехиометрия накопления энергии
Hoehler, T. M., and B. B. J?rgensen Microbial life under extreme energy limitation // Nature Reviews in Microbiology 11: 83–94 (2013).
Lane, N. Why are cells powered by proton gradients? // Nature Education 3: 18 (2010).
Martin, W., and M. J. Russell On the origin of biochemistry at an alkaline hydrothermal vent // Phil. Trans. R. Soc. B 367: 1887–1925 (2007).
Thauer, R. K., Kaster, A.-K., Seedorf, H., Buckel, W., and R. Hedderich Methanogenic archaea: ecologically relevant differences in energy conservation // Nature Reviews Microbiology 6: 579–591 (2007).
Вирусная инфекция и клеточная смерть
Bidle, K. D., and P. G. Falkowski Cell death in planktonic, photosynthetic microorganisms // Nature Reviews Microbiology 2: 643–655 (2004).
Lane, N. Origins of death // Nature 453: 583–585 (2008).
Refardt, D., Bergmiller, T., and R. K?mmerli Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection // Proc. R. Soc. B 280: 20123035 (2013).
Vardi, A., Formiggini, F., Casotti, R., De Martino, A., Ribalet, F., Miralto, A., and C. Bowler A stress surveillance system based on calcium and nitroc oxide in marine diatoms // PLoS Biology 4 (3): e60 (2006).
Соотношение площади поверхности и объема у бактерий
Fenchel, T., and B. J. Finlay Respiration rates in heterotrophic, free-living protozoa // Microbial Ecology 9: 99–122 (1983).
Harold, F. The Vital Force: a Study of Bioenergetics. W. H. Freeman, New York (1986).
Lane, N., and W. Martin The energetics of genome complexity // Nature 467: 929–934 (2010).
Lane, N. Energetics and genetics across the prokaryote-eukaryote divide // Biology Direct 6: 35 (2011).
Makarieva, A. M., Gorshkov, V. G., and B. L. Li Energetics of the smallest: do bacteria breathe at the same rate as whales? // Proc. R. Soc. B 272: 2219–2224 (2005).
Vellai, T., and G. Vida The origin of eukaryotes: the difference between prokaryotic and eukaryotic cells // Proc. R. Soc. B 266: 1571–1577 (1999).
Гигантские бактерии
Angert, E. R. DNA replication and genomic architecture of very large bacteria // Annual Review Microbiology 66: 197–212 (2012).
Mendell, J. E., Clements, K. D., Choat, J. H., and E. R. Extreme polyploidy in a large bacterium // Proceedings National Academy Sciences USA 105: 6730–6734 (2008).
Schulz, H. N., and B. B. Jorgensen Big bacteria // Annual Review Microbiology 55: 105–137 (2001).
Schulz, H. N. The genus Thiomargarita // Prokaryotes 6: 1156–1163 (2006).
Незначительная величина геномов эндосимбионтов и как это сказывается на энергии
Gregory, T. R., and R. DeSalle Comparative genomics in prokaryotes / In: The Evolution of the Genome. Gregory, T. R., ed. Elsevier, San Diego, pp. 585–575 (2005).
Lane, N., and W. Martin The energetics of genome complexity // Nature 467: 929–934 (2010).
Lane, N. Bioenergetic constraints on the evolution of complex life // Cold Spring Harbor Perspectives in Biology, doi: 10.1101/cshperspect.a015982 (2014).
Эндосимбионты в бактериях
Dohlen, C. D. von, Kohler, S., Alsop, S. T., and W. R. McManus Mealybug beta-proteobacterial symbionts contain gamma-proteobacterial symbionts // Nature 412: 433–436 (2001).
Почему у митохондрий сохранились собственные гены
Alberts, A., Johnson, A., Lewis, J., Raff, M., Roberts, K., and P. Walter Molecular Biology of the Cell. 5th edn. Garland Science, New York (2008).
Allen, J. F. Control of gene expression by redox potential and the requirement for chloroplast and mitochondrial genomes // Journal of Theoretical Biology 165: 609–631 (1993).
Allen, J. F. The function of genomes in bioenergetic organelles // Phil. Trans. R. Soc. B 358: 19–37 (2003).
Gray, M. W., Burger, G., and B. F. Lang Mitochondrial evolution // Science 283: 1476–1481 (1999).
Grey, A. D. de Forces maintaining organellar genomes: is any as strong as genetic code disparity or hydrophobicity? // BioEssays 27: 436–446 (2005).
Полиплоидия у цианобактерий
Griese, M., Lange, C., and J. Soppa Ploidy in cyanobacteria // FEMS Microbiology Letters 323: 124–131 (2011).
Почему на пластиды действуют те же энергетические ограничения, что на бактерии
Lane, N. Bioenergetic constraints on the evolution of complex life // Cold Spring Harbor Perspectives in Biology, doi: 10.1101/cshperspect.a015982 (2014).
Lane, N. Energetics and genetics across the prokaryote-eukaryote divide // Biology Direct 6: 35 (2011).
Конфликт направлений действия естественного отбора на разных уровнях и решение этой проблемы в рамках эндосимбиоза
Blackstone, N. W. Why did eukaryotes evolve only once? Genetic and energetic aspects of conflict and conflict mediation // Phil. Trans. R. Soc. B 368: 20120266 (2013).
Martin, W., and M. M?ller The hydrogen hypothesis for the first eukaryote // Nature 392: 37–41 (1998).
Бактерии и использование энергии
Russell, J. B. The energy spilling reactions of bacteria and other organisms // Journal of Molecular Microbiology and Biotechnology 13: 1–11 (2007).
Глава 6.
Половое размножение и происхождение смерти
Скорость эволюции
Conway-Morris, S. The Cambrian “explosion”: Slow-fuse or megatonnage? // Proceedings National Academy Sciences USA 97: 4426–4429 (2000).
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Nilsson, D.-E., and S. Pelger A pessimistic estimate of the time required for an eye to evolve // Proc. R. Soc. B 256: 53–58 (1994).
Половое размножение и структура популяции
Lahr, D. J., Parfrey, L. W., Mitchell, E. A., Katz, L. A., and E. Lara The chastity of amoeba: re-evaluating evidence for sex in amoeboid organisms // Proc. R. Soc. B 278: 2081–2090 (2011).
Maynard-Smith, J. The Evolution of Sex. Cambridge University Press, Cambridge (1978).
Ramesh, M. A., Malik, S. B., and J. M. Logsdon A phylogenomic inventory of meiotic genes: evidence for sex in Giardia and an early eukaryotic origin of meiosis // Current Biology 15: 185–191 (2005).
Takeuchi, N., Kaneko, K., and E. V. Koonin Horizontal gene transfer can rescue prokaryotes from Muller’s ratchet: benefit of DNA from dead cells and population subdivision // Genes Genomes Genetics 4: 325–339 (2014).
Происхождение интронов
Cavalier-Smith, T. Intron phylogeny: A new hypothesis // Trends in Genetics 7: 145–148 (1991).
Doolittle, W. F. Genes in pieces: were they ever together? // Nature 272: 581–582 (1978).
Koonin, E. V. The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate? // Biology Direct 1: 22 (2006).
Lambowitz, A. M., and S. Zimmerly Group II introns: mobile ribozymes that invade DNA // Cold Spring Harbor Perspectives in Biology 3: a003616 (2011).
Интроны и происхождение ядра
Koonin, E. Intron-dominated genomes of early ancestors of eukaryotes // Journal of Heredity 100: 618–623 (2009).
Martin, W., and E. V. Koonin Introns and the origin of nucleus – cytosol compartmentalization // Nature 440: 41–45 (2006).
Rogozin, I. B., Wokf, Y. I., Sorokin, A. V., Mirkin, B. G., and E. V. Koonin Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution // Current Biology 13: 1512–1517 (2003).
Wujek, D. E. Intracellular bacteria in the blue-green-alga Pleurocapsa minor // Transactions American Microscopical Society 98: 143–145 (1979).
Sverdlov, A. V., Csuros, M., Rogozin, I. B., and E. V. Koonin A glimpse of a putative pre-intron phase of eukaryotic evolution // Trends in Genetics 23: 105–108 (2007).
Ядерно-митохондриальные псевдогены
Hazkani-Covo, E., Zeller, R. M., and W. Martin Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes // PLoS Genetics 6: e1000834 (2010).
Lane, N. Plastids, genomes and the probability of gene transfer // Genome Biology and Evolution 3: 372–374 (2011).
Отбор против интронов
Lane, N. Energetics and genetics across the prokaryote-eukaryote divide // Biology Direct 6: 35 (2011).
Lynch, M., and A. O. Richardson The evolution of spliceosomal introns // Current Opinion in Genetics and Development 12: 701–710 (2002).
Скорость сплайсинга по сравнению со скоростью трансляции
Cavalier-Smith, T. Intron phylogeny: A new hypothesis // Trends in Genetics 7: 145–148 (1991).
Martin, W., and E. V. Koonin Introns and the origin of nucleus – cytosol compartmentalization // Nature 440: 41–45 (2006).
Происхождение ядерной мембраны, поровых комплексов и ядрышка
Mans, B. J., Anantharaman, V., Aravind, L., and E. V. Koonin Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex // Cell Cycle 3: 1612–1637 (2004).
Martin, W. A briefly argued case that mitochondria and plastids are descendants of endosymbionts, but that the nuclear compartment is not // Proc. R. Soc. B 266: 1387–1395 (1999).
Martin, W. Archaebacteria (Archaea) and the origin of the eukaryotic nucleus // Current Opinion in microbiology 8: 630–637 (2005).
McInerney J. O., Martin, W. F., Koonin, E. V., Allen, J. F., Galperin, M. Y., Lane, N., Archibald, J. M., and T. M. Embley Planctomycetes and eukaryotes: A case of analogy not homology // BioEssays 33: 810–817 (2011).
Mercier, R., Kawai, Y., and J. Errington Excess membrane synthesis drives a primitive mode of cell proliferation // Cell 152: 997–1007 (2013).
Staub, E., Fiziev, P., Rosenthal, A., and B. Hinzmann Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire // BioEssays 26: 567–581 (2004).
Эволюция секса
Bell, G. The Masterpiece of Nature: The Evolution and Genetics of Sexuality. University of California Press, Berkeley (1982).
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Hamilton, W. D. Sex versus non-sex versus parasite // Oikos 35: 282–290 (1980).
Lane, N. Why sex is worth losing your head for // New Scientist 2712: 40–43 (2009).
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Partridge, L., and L. D. Hurst Sex and conflict // Science 281: 2003–2008 (1998).
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Происхождение слияния клеток и хромосомной сегрегации
Blackstone, N. W., and D. R. Green The evolution of a mechanism of cell suicide // BioEssays 21: 84–88 (1999).
Ebersbach, G., and K. Gerdes Plasmid segregation mechanisms // Annual Review Genetics 39: 453–479 (2005).
Errington, J. L-form bacteria, cell walls and the origins of life // Open Biology 3: 120143 (2013).
Два пола
Fisher RA. The Genetical Theory of Natural Selection. Clarendon Press, Oxford (1930).
Hoekstra, R. F. On the asymmetry of sex – evolution of mating types in isogamous populations // Journal of Theoretical Biology 98: 427–451 (1982).
Hurst, L. D., and W. D. Hamilton Cytoplasmic fusion and the nature of sexes // Proc. R. Soc. B 247: 189–194 (1992).
Hutson V, Law R. Four steps to two sexes // Proc. R. Soc. B 253: 43–51 (1993).
Parker, G. A., Smith, V. G. F., and R. R. Baker The origin and evolution of gamete dimorphism and the male-female phenomenon // Journal of Theoretical Biology 36: 529–553 (1972).
Однородительское наследование митохондрий
Birky, C. W. Uniparental inheritance of mitochondrial and chloroplast genes – mechanisms and evolution // Proceedings National Academy Sciences USA 92: 11331–11338 (1995).
Cosmides, L. M., and J. Tooby Cytoplasmic inheritance and intragenomic conflict // Journal of Theoretical Biology 89: 83–129 (1981).
Hadjivasiliou, Z., Lane, N., Seymour, R., and A. Pomiankowski Dynamics of mitochondrial inheritance in the evolution of binary mating types and two sexes // Proc. R. Soc. B 280: 20131920 (2013).
Hadjivasiliou, Z., Pomiankowski, A., Seymour, R., and N. Lane Selection for mitonuclear co-adaptation could favour the evolution of two sexes // Proc. R. Soc. B 279: 1865–18672 (2012).
Lane, N. Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press, Oxford (2005).
Скорость митохондриального мутагенеза у животных, растений и базальных метазоев
Galtier, N. The intriguing evolutionary dynamics of plant mitochondrial DNA // BMC Biology 9: 61 (2011).
Huang, D., Meier, R., Todd, P. A., and L. M. Chou Slow mitochondrial COI sequence evolution at the base of the metazoan tree and its implications for DNA barcoding // Journal of Molecular Evolution 66: 167–174 (2008).
Lane, N. On the origin of barcodes // Nature 462: 272–274 (2009).
Linnane, A. W., Ozawa, T., Marzuki, S., and M. Tanaka Mitochondrial DNA mutations as an important contributor to ageing and degenerative disease // Lancet 333: 642–645 (1989).
Pesole, G., Gissi, C., De Chirico, A., and C. Saccone Nucleotide substitution rate of mammalian mitochondrial genomes // Journal of Molecular Evolution 48: 427–434 (1999).
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Эпилог. Из глубины
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