Вопрос жизни. Энергия, эволюция и происхождение сложности

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., Lopez-Garcia, 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).