Opublikowane 25.05.2021
Słowa kluczowe
- darwinizm,
- Nowoczesna Synteza,
- genomika ewolucyjna,
- biologia systemowa,
- Postnowoczesna Synteza biologii ewolucyjnej
- dobór oczyszczający,
- neutralne procesy ewolucyjne,
- nieadaptacjonistyczna teoria ewolucji ...More
Utwór dostępny jest na licencji Creative Commons Uznanie autorstwa 4.0 Międzynarodowe.
Jak cytować
Abstrakt
Genomika porównawcza i biologia systemowa oferują niespotykane możliwości testowania głównych zasad biologii ewolucyjnej sformułowanych przez Darwina w O powstawaniu gatunków w 1859 roku i rozszerzonych sto lat później w ramach Nowoczesnej Syntezy. Badania w dziedzinie genomiki ewolucyjnej pokazują, że dobór naturalny stanowi tylko jedną z sił kształtujących ewolucję genomu i wcale nie występującą najczęściej, natomiast procesy nieadaptacyjne mają znacznie większe znaczenie niż wcześniej przypuszczano. Duży wkład horyzontalnego transferu genów i różnych samolubnych elementów genetycznych w ewolucję genomu podważa koncepcję drzewa życia. Adekwatny opis ewolucji wymaga bardziej złożonej koncepcji sieci lub „lasu” życia. Nie istnieje spójny trend ewolucji w kierunku większej złożoności genomowej, a kiedy złożoność wzrasta, wydaje się, że jest to raczej nieadaptacyjna konsekwencja ewolucji drogą słabego doboru oczyszczającego niż adaptacji. Odkryto rozmaite powszechniki ewolucji genomu, w tym niezmiennicze rozkłady tempa ewolucji pośród genów ortologowych z różnych genomów oraz rozmiarów rodzin genów paralogowych. Dostrzeżono też negatywną korelację między poziomem ekspresji genów a tempem ewolucji sekwencji. Niektóre z tych powszechników uzyskują wyjaśnienie dzięki zastosowaniu prostych, nieadaptacjonistycznych modeli ewolucji, co sugeruje, że w dość nieodległej przyszłości powstać może nowa synteza biologii ewolucyjnej.
Downloads
Bibliografia
- Adami Christoph, „What is Complexity?”, BioEssays 2002, vol. 24, s. 1085-1094.
- Amaral Paulo P., Dinger Marcel, Mercer Tim R., and Mattick John S., „The Eukaryotic Genome as an RNA Machine”, Science 2008, vol. 319, s. 1787-1789.
- Andersson Jan O., „Lateral Gene Transfer in Eukaryotes”, Cellular and Molecular Life Sciences 2005, vol. 62, s. 1182-1197.
- Andersson Jan O., Sjögren Åsa, Horner David S., Murphy Colleen A., Dyal Patricia L., Svärd Staffan G., Logsdon John M., Jr., Ragan Mark A., Hirt Robert P., and Roger Andrew J., „A Genomic Survey of the Fish Parasite Spironucleus salmonicida Indicates Genomic Plasticity Among Diplomonads and Significant Lateral Gene Transfer in Eukaryote Genome Evolution”, BMC Genomics 2007, vol. 8, no. 51.
- Andolfatto Peter, „Adaptive Evolution of Non-Coding DNA in Drosophila”, Nature 2005, vol. 437, s. 1149-1152.
- Angly Florent E., Felts Ben, Breitbart Mya, Salamon Peter, Edwards Robert A., Carlson Craig, Chan Amy M., Haynes Matthew, Kelley Scott, LIU Hong et al., „The Marine Viromes of Four Oceanic Regions”, PLoS Biology 2006, vol. 4, e368.
- Aravind L., Tatusov Roman L., Wolf Yuri I., Walker D.R., and Koonin Eugene V., „Evidence for Massive Gene Exchange Between Archaeal and Bacterial Hyperthermophiles”, Trends in Genetics 1998, vol. 14, s. 442-444.
- Argos Patrick, Kamer Gregory, Nicklin Martin J., and Wimmer Eckard, „Similarity in Gene Organization and Homology Between Proteins of Animal Picornaviruses and a Plant Comovirus Suggest Common Ancestry of These Virus Families”, Nucleic Acids Research 1984, vol. 12, s. 7251-7267.
- Artamonova Irena I. and Gelfand Mikhail S., „Comparative Genomics and Evolution of Alternative Splicing: The Pessimists’ Science”, Chemical Review 2007, vol. 107, s. 3407-3430.
- Bapteste Eric, susko Edward, Leigh Jessica W., Macleod Dave, Charlebois Robert L., and Doolittle W. Ford, „Do Orthologous Gene Phylogenies Really Support Tree-Thinking?”, BMC Evolutionary Biology 2005, vol. 5, no. 33.
- Bejerano Gill, Pheasant Michael, Makunin Igor, Stephen Stuart, Kent W. James, Mattick John S., and Haussler David, „Ultraconserved Elements in the Human Genome”, Science 2004, vol. 304, s. 1321-1325.
- Black Douglas L., „Mechanisms of Alternative Pre-Messenger RNA Splicing”, Annual Review of Biochemistry 2003, vol. 72, s. 291-336.
- Brochier Corinne, PhilippE Hene’, and De Melo Moreira Débora Regina, „The Evolutionary History of Ribosomal Protein RpS14: Horizontal Gene Transfer at the Heart of the Ribosome”, Trends in Genetics 2000, vol. 16, s. 529-533.
- Brown James R., „Genomic and Phylogenetic Perspectives on the Evolution of Prokaryotes”, Systematic Biology 2001, vol. 50, s. 497-512.
- Browne Janet, „Birthdays to Remember”, Nature 2008, vol. 456, s. 324-325.
- Bryson Vernon and Vogel Henry (eds.), Evolving Gene and Proteins, Academic Press, New York 1965.
- Bürglin Thomas R., „Evolution of Hedgehog and Hedgehog-Related Genes, Their Origin from Hog Proteins in Ancestral Eukaryotes and Discovery of a Novel Hint Motif”, BMC Genomics 2008, vol. 9, no. 127.
- Bushman Frederic, Lateral DNA Transfer: Mechanisms and Consequences, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York 2001.
- Cairns John, Stent Gunther S., and Watson James D. (eds.), Phage and the Origins of Molecular Biology, CSHL Press, Cold Spring Harbor, New York 1966.
- Carlton Jane M., Hirt Robert P., Silva Joana C., Delcher Arthur L., Schatz Michael, Zhao Qi, Wortman Jennifer R., Bidwell Shelby L., Alsmark U. Cecilia M., Besteiro Sébastien et al., „Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis”, Science 2007, vol. 315, s. 207-212.
- Carmel Liran, Wolf Yuri I., Rogozin Igor B., and Koonin Eugene V., „Three Distinct Modes of Intron Dynamics in the Evolution of Eukaryotes”, Genome Research 2007, vol. 17, s. 1034-1044.
- Castillo-Davis Cristian I., Kondrashov Fyodor A., Hartl Daniel L., and Kulathinal Rob J., „The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint”, Genome Research 2004, vol. 14, s. 802-811.
- Charlebois Robert L. and Doolittle W. Ford, „Computing Prokaryotic Gene Ubiquity: Rescuing the Core from Extinction”, Genome Research 2004, vol. 14, s. 2469-2477.
- Chen John Xi and Novick Richard P., „Phage-Mediated Intergeneric Transfer of Toxin Genes”, Science 2009, vol. 323, s. 139-141.
- Clark Andrew G., Eisen Michael B., Smith Douglas R., Bergman Casey M., Oliver Brian, Markow Therese A., Kaufman Thomas C., Kellis Manolis, Gelbart William, Iyer Venky N. et al., „Evolution of Genes and Genomes on the Drosophila Phylogeny”, Nature 2007, vol. 450, s. 203-218.
- Conant Gavin C. and Wolfe Kenneth H., „Turning a Hobby into a Job: How Duplicated Genes Find New Functions”, Nature Reviews Genetics 2008, vol. 9, s. 938-950.
- Crick Francis H., „On Protein Synthesis”, Symposia of the Society for Experimental Biology 1958, vol. 12, s. 138-163.
- Csűrös Miklós, Rogozin Igor B., and Koonin Eugene V., „Extremely Intron-Rich Genes in the Alveolate Ancestors Inferred with a Flexible Maximum-Likelihood Approach”, Molecular Biology and Evolution 2008, vol. 25, s. 903-911.
- Cutler David J., „Understanding the Overdispersed Molecular Clock”, Genetics 2000, vol. 154, s. 1403-1417.
- Dagan Tal and Martin William F., „Testing Hypotheses Without Considering Predictions”, BioEssays 2007, vol. 29, s. 500-503.
- Dagan Tal and Martin William F., „The Tree of One Percent”, Genome Biology 2006, vol. 7, no. 118.
- Darwin Charles, „On the Tendency of Species to Form Varieties; And on the Perpetuation of Varieties and Species by Natural Means of Selection. I. Extract from an Unpublished Work on Species, II. Abstract of a Letter from C. Darwin, esq., to Prof. Asa Gray”, Journal of the Proceedings of the Linnean Society of London 1858, vol. 3, s. 45-53.
- Darwin Karol, O powstawaniu gatunków drogą doboru naturalnego, czyli o utrzymaniu się doskonalszych ras w walce o byt, tekst polski na podstawie przekładu Szymona Dicksteina i Józefa Nusbauma opracowały Joanna Popiołek i Małgorzata Yamazaki, Wydawnictwa Uniwersytetu Warszawskiego, Warszawa 2009.
- Dawkins Richard, Samolubny gen, przeł. Marek Skoneczny, Na Ścieżkach Nauki, Prószyński i S-ka, Warszawa 1996.
- Dayhoff Margaret O., Barker Winona C., and Hunt Lois T., „Establishing Homologies in Protein Sequences”, Methods in Enzymology 1983, vol. 91, s. 524-545.
- Dayhoff Margaret O., Barker Winona C., and Mclaughlin Patrick J., „Inferences from Protein and Nucleic Acid Sequences: Early Molecular Evolution, Divergence of Kingdoms and Rates of Change”, Origins of Life 1974, vol. 5, s. 311-330.
- De Koning Anoek P., Brinkman Fiona S.L., Jones Steven J.M., and Keeling Patrick J., „Lateral Gene Transfer and Metabolic Adaptation in the Human Parasite Trichomonas vaginalis”, Molecular Biology and Evolution 2000, vol. 17, s. 1769-1773.
- De Lamarck Jean-Baptiste, Filozofia zoologii, przeł. Krystyna Zaćwilichowska, Polskie Wydawnictwo Naukowe, Warszawa 1960.
- Dehal Paramvir and Boore Jeffrey L., „Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate”, PLoS Biology 2005, vol. 3, e314.
- Delong Edward F. and Karl David M., „Genomic Perspectives in Microbial Oceanography”, Nature 2005, vol. 437, s. 336-342.
- Delwart Eric L., „Viral Metagenomics”, Reviews in Medical Virology 2007, vol. 17, s. 115-131.
- Dobzhansky Theodosius, Genetics and the Origin of Species, Columbia University Press, New York 1937.
- Doolittle W. Ford, „Phylogenetic Classification and the Universal Tree”, Science 1999, vol. 284, s. 2124-2129.
- Doolittle W. Ford and Bapteste Eric, „Pattern Pluralism and the Tree of Life Hypothesis”, Proceedings of the National Academy of Sciences USA 2007, vol. 104, s. 2043-2049.
- Doolittle W. Ford and Sapienza Carmen, „Selfish Genes, the Phenotype Paradigm and Genome Evolution”, Nature 1980, vol. 284, s. 601-603.
- Drummond D. Allan, Bloom Jesse D., Adami Christoph, Wilke Claus O., and Arnold Frances H., „Why Highly Expressed Proteins Evolve Slowly”, Proceedings of the National Academy of Sciences USA 2005, vol. 102, s. 14338-14343.
- Drummond D. Allan, Raval Alpan, and Wilke Claus O., „A Single Determinant Dominates the Rate of Yeast Protein Evolution”, Molecular Biology and Evolution 2006, vol. 23, s. 327-337.
- Drummond D. Allan and Wilke Claus O., „Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution”, Cell 2008, vol. 134, s. 341-352.
- Dunning Hotopp Julie C., Clark Michael E., Oliveira Deodoro C.S.G., Foster Jeremy M., Fischer Peter, Muñoz Torres Mónica C., Giebel Jonathan D., Kumar Nikhil, Ishmael Nadeeza, Wang Shiliang et al., „Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes”, Science 2007, vol. 317, s. 1753-1756.
- Durand Dannie, „Vertebrate Evolution: Doubling and Shuffling with a Full Deck”, Trends in Genetics 2003, vol. 19, s. 2-5.
- Eck Richard V. and Dayhoff Margaret O., „Evolution of the Structure of Ferredoxin Based on Living Relics of Primitive Amino Acid Sequences”, Science 1966, vol. 152, s. 363-366.
- Edwards Robert A. and Rohwer Forest, „Viral Metagenomics”, Nature Reviews Microbiology 2005, vol. 3, s. 504-510.
- Eisen Jonathan A. and Fraser Claire M., „Phylogenomics: Intersection of Evolution and Genomics”, Science 2003, vol. 300, s. 1706-1707.
- Eisen Jonathan A., Heidelberg John F., White Owen, and Salzberg Steven L., „Evidence for Symmetric Chromosomal Inversions Around the Replication Origin in Bacteria”, Genome Biology 2000, vol. 1, RESEARCH0011.
- Embley T. Martin, „Multiple Secondary Origins of the Anaerobic Lifestyle in Eukaryotes”, Philosophical Transactions of the Royal Society of London B: Biological Sciences 2006, vol. 361, s. 1055-1067.
- Embley T. Martin and Martin William, „Eukaryotic Evolution, Changes and Challenges”, Nature 2006, vol. 440, s. 623-630.
- Esser Christian, Ahmadinejad Nahal, Wiegand Christian, Rotte Carmen, Sebastiani Federico L., Gelius-Dietrich Gabriel, Henze Katrin, Kretschmann Ernst, Richly Erik, Leister Dario et al., „A Genome Phylogeny for Mitochondria Among Alpha-Proteobacteria and a Predominantly Eubacterial Ancestry of Yeast Nuclear Genes”, Molecular Biology and Evolution 2004, vol. 21, s. 1643-1660.
- Esser Christian, Martin William, and Dagan Tal, „The Origin of Mitochondria in Light of a Fluid Prokaryotic Chromosome Model”, Biology Letters 2007, vol. 3, s. 180-184.
- Fedorov Alexei, Merican Amir F., and Gilbert Walter, „Largescale Comparison of Intron Positions Among Animal, Plant, and Fungal Genes”, Proceedings of the National Academy of Sciences USA 2002, vol. 99, s. 16128-16133.
- Finnegan David J., „Transposable Elements in Eukaryotes”, International Review of Cytology 1985, vol. 93, s. 281-326.
- Fisher Ronald A., The Genetical Theory of Natural Selection, Clarendon Press, Oxford 1930.
- Fisher Ronald A., „The Possible Modification of the Response of the Wild Type to Recurrent Mutations”, The American Naturalist 1928, vol. 62, s. 115-126.
- Forterre Patrick, „The Origin of Viruses and Their Possible Roles in Major Evolutionary Transitions”, Virus Research 2006, vol. 117, s. 5-16.
- Fraser Claire M., Eisen Jonathan A., and Salzberg Steven L., „Microbial Genome Sequencing”, Nature 2000, vol. 406, s. 799-803.
- Freeling Michael, „The Evolutionary Position of Subfunctionalization, Downgraded”, Genome Dynamics 2008, vol. 4, s. 25-40.
- Frost Laura S., Leplae Raphael, Summers Anne O., and Toussaint Ariane, „Mobile Genetic Elements: The Agents of Open Source Evolution”, Nature Reviews Microbiology 2005, vol. 3, s. 722-732.
- Futuyma Douglas J., Ewolucja, przekł. pod red. Jacka Radwana, Wydawnictwa Uniwersytetu Warszawskiego, Warszawa 2008.
- Georgiev Georgii P., „Mobile Genetic Elements in Animal Cells and Their Biological Significance”, European Journal of Biochemistry 1984, vol. 145, s. 203-220.
- Georgiev Georgii P., Ilyin Y.V., Ryskov A.P., Tchurikov Nickolai A., Yenikolopov Grigori N., Gvozdev Vladimir A., and Ananiev E.V., „Isolation of Eukaryotic DNA Fragments Containing Structural Genes and the Adjacent Sequences”, Science 1977, vol. 195, s. 394-397.
- Glansdorff Nicholas, Xu Ying, and Labedan Bernard, „The Last Universal Common Ancestor: Emergence, Constitution and Genetic Legacy of an Elusive Forerunner”, Biology Direct 2008, vol. 3, no. 29.
- Glazko Galina V., Koonin Eugene V., Rogozin Igor B., and Shabalina Svetlana A., „A Significant Fraction of Conserved Noncoding DNA in Human and Mouse Consists of Predicted Matrix Attachment Regions”, Trends in Genetics 2003, vol. 19, s. 119-124.
- Glazko Galina V., Makarenkov Vladimir, Liu Jing, and Mushegian Arcady, „Evolutionary History of Bacteriophages with Double-Stranded DNA Genomes”, Biology Direct 2007, vol. 2, no. 36.
- Gogarten J. Peter, Doolittle W. Ford, and Lawrence Jeffrey G., „Prokaryotic Evolution in Light of Gene Transfer”, Molecular Biology and Evolution 2002, vol. 19, s. 2226-2238.
- Gogarten J. Peter and Townsend Jeffrey P., „Horizontal Gene Transfer, Genome Innovation and Evolution”, Nature Reviews Microbiology 2005, vol. 3, s. 679-687.
- Goldbach Rob, „Genome Similarities Between Plant and Animal RNA Viruses”, Microbiological Sciences 1987, vol. 4, s. 197-202.
- Goodier John L. and Kazazian Haig H., Jr., „Retrotransposons Revisited: The Restraint and Rehabilitation of Parasites”, Cell 2008, vol. 135, s. 23-35.
- Gould Stephen Jay, Full House: The Spread of Excellence from Plato to Darwin, Three Rivers Press, New York 1997.
- Gould Stephen Jay, „The Exaptive Excellence of Spandrels as a Term and Prototype”, Proceedings of the National Academy of Sciences USA 1997, vol. 94, s. 10750-10755.
- Gould Stephen Jay, The Structure of Evolutionary Theory, Harvard University Press, Cambridge, Massachusetts 2002.
- Gould Stephen Jay and Lewontin Richard C., „The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme”, Proceedings of the Royal Society of London B: Biological Sciences 1979, vol. 205, s. 581-598.
- Gray Michael W., „The Endosymbiont Hypothesis Revisited”, International Review of Cytology 1992, vol. 141, s. 233-357.
- Gray Michael W., Burger Gertraud, and Lang B. Franz, „The Origin and Early Evolution of Mitochondria”, Genome Biology 2001, vol. 2, no. 6.
- Grishin Nick V., Wolf Yuri I., and Koonin Eugene V., „From Complete Genomes to Measures of Substitution Rate Variability Within and Between Proteins”, Genome Research 2000, vol. 10, s. 991-1000.
- Hacker Jörg H. and Kaper James B., „Pathogenicity Islands and the Evolution of Microbes”, Annual Review of Microbiology 2000, vol. 54, s. 641-679.
- Haddrill Penelope R., Bachtrog Doris, and Andolfatto Peter, „Positive and Negative Selection on Noncoding DNA in Drosophila simulans”, Molecular Biology and Evolution 2008, vol. 25, s. 1825-1834.
- Haeckel Ernst, The Wonders of Life: A Popular Study of Biological Philosophy, Watts & Co., London 1904.
- Haldane John B.S., The Causes of Evolution, Longmans, Green & Co., London 1932.
- Hall Tracy M., Porter Jeffery A., Young Keith E., Koonin Eugene V., Beachy Philip A., and Leahy Daniel J., „Crystal Structure of a Hedgehog Autoprocessing Domain: Homology Between Hedgehog and Self-Splicing Proteins”, Cell 1997, vol. 91, s. 85-97.
- Halligan Daniel L. and Keightley Peter D., „Ubiquitous Selective Constraints in the Drosophila Genome Revealed by a Genome-Wide Interspecies Comparison”, Genome Research 2006, vol. 16, s. 875-884.
- Harris J. Kirk, Kelley Scott T., Spiegelman George B., and Pace Norman R., „The Genetic Core of the Universal Ancestor”, Genome Research 2003, vol. 13, s. 407-412.
- Hartl Daniel L., „Molecular Melodies in High and Low C”, Nature Reviews Genetics 2000, vol. 1, s. 145-149.
- He Xionglei and Zhang Jianzhi, „Rapid Subfunctionalization Accompanied by Prolonged and Substantial Neofunctionalization in Duplicate Gene Evolution”, Genetics 2005, vol. 169, s. 1157-1164.
- Hillenmeyer Maureen E., Fung Eula, Wildenhain Jan, Pierce Sarah E., Hoon Shawn, Lee William, Proctor Michael, Onge Robert P. St., Tyers Mike, Koller Daphne et al., „The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes”, Science 2008, vol. 320, s. 362-365.
- Hirsh Aaron E. and Fraser Hunter B., „Protein Dispensability and Rate of Evolution”, Nature 2001, vol. 411, s. 1046-1049.
- Hoegg Simone and Meyer Axel, „Hox Clusters as Models for Vertebrate Genome Evolution”, Trends in Genetics 2005, vol. 21, s. 421-424.
- Hurst Laurence D., Pál Csaba, and Lercher Martin J., „The Evolutionary Dynamics of Eukaryotic Gene Order”, Nature Reviews Genetics 2004, vol. 5, s. 299-310.
- Hurst Laurence D. and Smith Nick G.C., „Do Essential Genes Evolve Slowly?”, Current Biology 1999, vol. 9, s. 747-750.
- Huxley Julian S., Evolution: The Modern Synthesis, Allen and Unwin, London 1942.
- Huynen Martijn A. and Van Nimwegen Erik, „The Frequency Distribution of Gene Family Sizes in Complete Genomes”, Molecular Biology and Evolution 1998, vol. 15, s. 583-589.
- Irimia Manuel, Penny David, and Roy Scott W., „Coevolution of Genomic Intron Number and Splice Sites”, Trends in Genetics 2007, vol. 23, s. 321-325.
- Itoh Takeshi, Takemoto Keiko, Mori Hirotada, and Gojobori Takashi, „Evolutionary Instability of Operon Structures Disclosed by Sequence Comparisons of Complete Microbial Genomes”, Molecular Biology and Evolution 1999, vol. 16, s. 332-346.
- Iyer Lakshminarayan M., Balaji Sandhiya, Koonin Eugene V., and Aravind L., „Evolutionary Genomics of Nucleo-Cytoplasmic Large DNA Viruses”, Virus Research 2006, vol. 117, s. 156-184.
- Iyer Lakshminarayan M., Koonin Eugene V., and Aravind L., „Evolution of Bacterial RNA Polymerase: Implications for Large-Scale Bacterial Phylogeny, Domain Accretion, and Horizontal Gene Transfer”, Gene 2004, vol. 335, s. 73-88.
- Iyer Lakshminarayan M., Makarova Kira S., Koonin Eugene V., and Aravind L., „Comparative Genomics of the FtsK-HerA Superfamily of Pumping ATPases: Implications for the Origins of Chromosome Segregation, Cell Division and Viral Capsid Packaging”, Nucleic Acids Research 2004, vol. 32, s. 5260-5279.
- Jacob François, „Evolution and Tinkering”, Science 1977, vol. 196, s. 1161-1166.
- Jaillon Olivier, Bouhouche Khaled, Gout Jean-François, Aury Jean-Marc, Noel Benjamin, Saudemont Baptiste, Nowacki Mariusz, Serrano Vincent, Porcel Betina M., Ségurens Béatrice et al., „Translational Control of Intron Splicing in Eukaryotes”, Nature 2008, vol. 451, s. 359-362.
- Jain Ravi, Rivera Maria C., and Lake James A., „Horizontal Gene Transfer Among Genomes: The Complexity Hypothesis”, Proceedings of the National Academy of Sciences USA 1999, vol. 96, s. 3801-3806.
- Jordan I. King, Mariño-Ramírez Leonardo, and Koonin Eugene V., „Evolutionary Significance of Gene Expression Divergence”, Gene 2005, vol. 345, s. 119-126.
- Jordan I. King, Mariño-Ramírez Leonardo, Wolf Yuri I., and Koonin Eugene V., „Conservation and Coevolution in the Scale-Free Human Gene Coexpression Network”, Molecular Biology and Evolution 2004, vol. 21, s. 2058-2070.
- Jordan I. King, Rogozin Igor B., Glazko Galina V., and KOONIN Eugene V., „Origin of a Substantial Fraction of Human Regulatory Sequences from Transposable Elements”, Trends in Genetics 2003, vol. 19, s. 68-72.
- Jordan I. King, Rogozin Igor B., Wolf Yuri I., and Koonin Eugene V., „Essential Genes Are More Evolutionarily Conserved Than Are Nonessential Genes in Bacteria”, Genome Research 2002, vol. 12, s. 962-968.
- Jordan I. King, Rogozin Igor B., Wolf Yuri I., and Koonin Eugene V., „Microevolutionary Genomics of Bacteria”, Theoretical Population Biology 2002, vol. 61, s. 435-447.
- Kamer Gregory and Argos Patrick, „Primary Structural Comparison of RNA-Dependent Polymerases from Plant, Animal and Bacterial Viruses”, Nucleic Acids Research 1984, vol. 12, s. 7269-7282.
- Karev Georgy P., Wolf Yuri I., Rzhetsky Andrey Y., Berezovskaya Faina S., and Koonin Eugene V., „Birth and Death of Protein Domains: A Simple Model of Evolution Explains Power Law Behavior”, BMC Evolutionary Biology 2002, vol. 2, no. 18.
- Karl David M., „Microbial Oceanography: Paradigms, Processes and Promise”, Nature Reviews Microbiology 2007, vol. 5, s. 759-769.
- Kasha Michael and Pullman Bernard (eds.), Horizons in Biochemistry, Academic Press, New York 1962.
- Katzman Sol, Kern Andrew D., Bejerano Gill, Fewell Ginger, Fulton Lucinda, Wilson Richard K., Salama Sofie R., and Haussler David, „Human Genome Ultraconserved Elements Are Ultraselected”, Science 2007, vol. 317, s. 915.
- Kelley Lawrence L. and Scott Michael, „The Evolution of Biology: A Shift Towards the Engineering of Prediction-Generating Tools and Away from Traditional Research Practice”, EMBO Reports 2008, vol. 9, s. 1163-1167.
- Khaitovich philipp, Enard Wolfgang, Lachmann Michael, and Pääbo Svante, „Evolution of Primate Gene Expression”, Nature Reviews Genetics 2006, vol. 7, s. 693-702.
- Kimura Motoo, „Evolutionary Rate at the Molecular Level”, Nature 1968, vol. 217, s. 624-626.
- Kimura Motoo, „Recent Development of the Neutral Theory Viewed from the Wrightian Tradition of Theoretical Population Genetics”, Proceedings of the National Academy of Sciences USA 1991, vol. 88, s. 5969-5973.
- Kimura Mooto, The Neutral Theory of Molecular Evolution, Cambridge University Press, Cambridge 1983.
- King Jack L. and Jukes Thomas H., „Non-Darwinian Evolution”, Science 1969, vol. 164, s. 788-798.
- Kondrashov Fyodor A. and Koonin Eugene V., „Evolution of Alternative Splicing: Deletions, Insertions and Origin of Functional Parts of Proteins from Intron Sequences”, Trends in Genetics 2003, vol. 19, s. 115-119.
- Kondrashov Fyodor A., Koonin Eugene V., Morgunov Igor G., Finogenova Tatiana V., and Kondrashova Marie N., „Evolution of Glyoxylate Cycle Enzymes in Metazoa: Evidence of Multiple Horizontal Transfer Events and Pseudogene Formation”, Biology Direct 2006, vol. 1, no. 31.
- Kondrashov Fyodor A., Rogozin Igor B., Wolf Yuri I., and Koonin Eugene V., „Selection in the Evolution of Gene Duplications”, Genome Biology 2002, vol. 3, RESEARCH0008.
- Koonin Eugene V., „A Non-Adaptationist Perspective on Evolution of Genomic Complexity Or the Continued Dethroning of Man”, Cell Cycle 2004, vol. 3, s. 280-285.
- Koonin Eugene V., „Comparative Genomics, Minimal Gene-Sets and the Last Universal Common Ancestor”, Nature Reviews Microbiology 2003, vol. 1, s. 127-136.
- Koonin Eugene V., „Evolution of Genome Architecture”, The International Journal of Biochemistry and Cell Biology 2009, vol. 41, s. 298-306.
- Koonin Eugene V., „Horizontal Gene Transfer: The Path to Maturity”, Molecular Microbiology 2003, vol. 50, s. 725-727.
- Koonin Eugene V., „On the Origin of Cells and Viruses: Primordial Virus World Scenario”, Annals of the New York Academy of Sciences 2009, vol. 1178, s. 47-64.
- Koonin Eugene V., „The Biological Big Bang Model for the Major Transitions in Evolution”, Biology Direct 2007, vol. 2, no. 21.
- Koonin Eugene V. and Dolja Valerian V., „Evolution and Taxonomy of Positive-Strand RNA Viruses: Implications of Comparative Analysis of Amino Acid Sequences”, Critical Reviews in Biochemistry and Molecular Biology 1993, vol. 28, s. 375-430.
- Koonin Eugene V., Fedorova Natalie D., Jackson John D., Jacobs Aviva R., Krylov Dmitri M., Makarova Kira S., Mazumder Raja, Mekhedov Sergei L., Nikolskaya Anastasia N., RAO B. Sridhar et al., „A Comprehensive Evolutionary Classification of Proteins Encoded in Complete Eukaryotic Genomes”, Genome Biology 2004, vol. 5, s. R7.
- Koonin Eugene V. and Martin William, „On the Origin of Genomes and Cells Within Inorganic Compartments”, Trends in Genetics 2005, vol. 21, s. 647-654.
- Koonin Eugene V. and Mushegian Arcady R., „Complete Genome Sequences of Cellular Life Forms: Glimpses of Theoretical Evolutionary Genomics”, Current Opinion in Genetics and Development 1996, vol. 6, s. 757-762.
- Koonin Eugene V., Mushegian Arcady R., and Rudd Kenneth E., „Sequencing and Analysis of Bacterial Genomes”, Current Biology 1996, vol. 6, s. 404-416.
- Koonin Eugene V., Senkevich Tatiana G., and Dolja Valerian V., „The Ancient Virus World and Evolution of Cells”, Biology Direct 2006, vol. 1, no. 29.
- Koonin Eugene V. and Wolf Yuri I., „Evolutionary Systems Biology”, w: PAGEL and Pomiankowski, (eds.), Evolutionary Genomics…, s. 11-25.
- Koonin Eugene V. and Wolf Yuri I., „Evolutionary Systems Biology: Links Between Gene Evolution and Function”, Current Opinion in Biotechnology 2006, vol. 17, s. 481-487.
- Koonin Eugene V. and Wolf Yuri I., „Genomics of Bacteria and Archaea: The Emerging Dynamic View of the Prokaryotic World”, Nucleic Acids Research 2008, vol. 36, s. 6688-6719.
- Koonin Eugene V. and Wolf Yuri I., „Genomics of Bacteria and Archaea: The Emerging Generalizations After 13 Years”, Nucleic Acids Research 2008, vol. 36, s. 6688-6719.
- Koonin Eugene V., Wolf Yuri I., and Karev Georgy P. (eds.), Power Laws, Scale-Free Networks and Genome Biology, Landes Bioscience, Georgetown, Texas 2006.
- Koonin Eugene V., Wolf Yuri I., and Karev Georgy P., „The Structure of the Protein Universe and Genome Evolution”, Nature 2002, vol. 420, s. 218-223.
- Koonin Eugene V., Wolf Yuri I., Nagasaki Keizo, and Dolja Valerian V., „The Big Bang of Picorna-Like Virus Evolution Antedates the Radiation of Eukaryotic Supergroups”, Nature Reviews Microbiology 2008, vol. 6, s. 925-939.
- Kosiol Carolin, Vinař Tomáš, Da Fonseca Rute R., Hubisz Melissa J., Bustamante Carlos D., Nielsen Rasmus, and Siepel Adam, „Patterns of Positive Selection in Six Mammalian Genomes”, PLoS Genetics 2008, vol. 4, e1000144.
- Kreitman Martin, „Methods to Detect Selection in Populations with Applications to the Human”, Annual Review of Genomics and Human Genetics 2000, vol. 1, s. 539-559.
- Krylov Dmitri M., Wolf Yuri I., Rogozin Igor B., and Koonin Eugene V., „Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution”, Genome Research 2003, vol. 13, s. 2229-2235.
- Kunin Victor and Ouzounis Christos A., „The Balance of Driving Forces During Genome Evolution in Prokaryotes”, Genome Research 2003, vol. 13, s. 1589-1594.
- Kurland Charles G., Canbäck Björn, and Berg Otto G., „Horizontal Gene Transfer: A Critical View”, Proceedings of the National Academy of Sciences USA 2003, vol. 100, s. 9658-9662.
- Kurland Charles G., Collins Laura J., and Penny David, „Genomics and the Irreducible Nature of Eukaryote Cells”, Science 2006, vol. 312, s. 1011-1014.
- Langer Martin, Gabor Esther M., Liebeton Klaus, Meurer Guido, Niehaus Frank, Schulze Renate, Eck Jürgen, and Lorenz Patrick, „Metagenomics: An Inexhaustible Access to Nature’s Diversity”, Biotechnology Journal 2006, vol. 1, s. 815-821.
- Lawrence Jeffrey G., „Gene Organization: Selection, Selfishness, and Serendipity”, Annual Review of Microbiology 2003, vol. 57, s. 419-440.
- Lawrence Jeffrey G., „Selfish Operons and Speciation by Gene Transfer”, Trends in Microbiology 1997, vol. 5, s. 355-359.
- Lawrence Jeffrey G., „Selfish Operons: The Evolutionary Impact of Gene Clustering in Prokaryotes and Eukaryotes”, Current Opinion in Genetics and Development 1999, vol. 9, s. 642-648.
- Lawrence Jeffrey G. and Hendrickson Heather L., „Lateral Gene Transfer: When Will Adolescence End?”, Molecular Microbiology 2003, vol. 50, s. 739-749.
- Lazcano Antonio and Forterre Patrick, „The Molecular Search for the Last Common Ancestor”, Journal of Molecular Evolution 1999, vol. 49, s. 411-412.
- Leipe Detlef D., Aravind L., and Koonin Eugene V., „Did DNA Replication Evolve Twice Independently?”, Nucleic Acids Research 1999, vol. 27, s. 3389-3401.
- Liao Ben-Yang and Zhang Jianzhi, „Evolutionary Conservation of Expression Profiles Between Human and Mouse Orthologous Genes”, Molecular Biology and Evolution 2006, vol. 23, s. 530-540.
- Liao Ben-Yang and Zhang Jianzhi, „Low Rates of Expression Profile Divergence in Highly Expressed Genes and Tissue-Specific Genes During Mammalian Evolution”, Molecular Biology and Evolution 2006, vol. 23, s. 1119-1128.
- Linnemann Amelia K., Platts Adrian E., and Krawetz Stephen A., „Differential Nuclear Scaffold/Matrix Attachment Marks Expressed Genes”, Human Molecular Genetics 2009, vol. 18, s. 645-654.
- Liolios Konstantinos, Mavromatis Konstantinos, Tavernarakis Nektarios, and Kyrpides Nikos C., „The Genomes On Line Database (GOLD) in 2007: Status of Genomic and Metagenomic Projects and Their Associated Metadata”, Nucleic Acids Research 2008, vol. 36, s. D475-D479.
- Long Manyuan, Betrán Esther, Thornton Kevin, and Wang Wen, „The Origin of New Genes: Glimpses from the Young and Old”, Nature Reviews Genetics 2003, vol. 4, s. 865-875.
- Lunter Gerton, Ponting Chris P., and Hein Jotun, „Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model”, PLoS Computational Biology 2006, vol. 2, e5.
- Lynch Michael, „The Frailty of Adaptive Hypotheses for the Origins of Organismal Complexity”, Proceedings of the National Academy of Sciences USA 2007, vol. 104, suppl. 1, s. 8597-8604.
- Lynch Michael, The Origins of Genome Architecture, Sinauer Associates, Sunderland, Massachusetts 2007.
- Lynch Michael and Conery John S., „The Evolutionary Fate and Consequences of Duplicate Genes”, Science 2000, vol. 290, s. 1151-1155.
- Lynch Michael and Conery John S., „The Origins of Genome Complexity”, Science 2003, vol. 302, s. 1401-1404.
- Lynch Michael and Force Allan, „The Probability of Duplicate Gene Preservation by Subfunctionalization”, Genetics 2000, vol. 154, s. 459-473.
- Lynch Michael and Katju Vaishali, „The Altered Evolutionary Trajectories of Gene Duplicates”, Trends in Genetics 2004, vol. 20, s. 544-549.
- Lynch Michael and Kewalramani Avinash, „Messenger RNA Surveillance and the Evolutionary Proliferation of Introns”, Molecular Biology and Evolution 2003, vol. 20, s. 563-571.
- Lyons Sherrie L., Thomas Henry Huxley: The Evolution of a Scientist, Prometheus, Amherst — New York 2000.
- Makałowski Wojciech and Boguski Mark S., „Evolutionary Parameters of the Transcribed Mammalian Genome: An Analysis of 2,820 Orthologous Rodent and Human Sequences”, Proceedings of the National Academy of Sciences USA 1998, vol. 95, s. 9407-9412.
- Makarova Kira S., Ponomarev V.A., and Koonin Eugene V., „Two C Or Not Two C: Recurrent Disruption of Zn-Ribbons, Gene Duplication, Lineage-Specific Gene Loss, and Horizontal Gene Transfer in Evolution of Bacterial Ribosomal Proteins”, Genome Biology 2001, vol. 2, RESEARCH0033.
- Makarova Kira S., Slesarev Alexei I., Wolf Yuri I., Sorokin Alexander V., Mirkin Boris G., Koonin Eugene V., Pavlov Andrey, Pavlova N., Karamychev V., Polouchine N. et al., „Comparative Genomics of the Lactic Acid Bacteria”, Proceedings of the National Academy of Sciences USA 2006, vol. 103, s. 15611-15616.
- Makarova Kira S., Sorokin Alexander V., Novichkov Pavel S., Wolf Yuri I., and Koonin Eugene V., „Clusters of Orthologous Genes for 41 Archaeal Genomes and Implications for Evolutionary Genomics of Archaea”, Biology Direct 2007, vol. 2, no. 33.
- Makarova Kira S., Wolf Yuri I., Mekhedov Sergey L., Mirkin Boris G., and Koonin Eugene V., „Ancestral Paralogs and Pseudoparalogs and Their Role in the Emergence of the Eukaryotic Cell”, Nucleic Acids Research 2005, vol. 33, s. 4626-4638.
- Martin Whitney, Hoffmeister Meike, Rotte Carmen, and Henze Katrin, „An Overview of Endosymbiotic Models for the Origins of Eukaryotes, Their ATP-Producing Organelles (Mitochondria and Hydrogenosomes), and Their Heterotrophic Lifestyle”, Biological Chemistry 2001, vol. 382, s. 1521-1539.
- Martin William and Koonin Eugene V., „Introns and the Origin of Nucleus-Cytosol Compartmentation”, Nature 2006, vol. 440, s. 41-45.
- Martin William and Müller Miklós, „The Hydrogen Hypothesis for the First Eukaryote”, Nature 1998, vol. 392, s. 37-41.
- Martin William, Rujan Tamas, Richly Erik, Hansen Andrea, Cornelsen Sabine, Lins Thomas, Leister Dario, Stoebe Bettina, Hasegawa Masami, and Penny David, „Evolutionary Analysis of Arabidopsis, Cyanobacterial, and Chloroplast Genomes Reveals Plastid Phylogeny and Thousands of Cyanobacterial Genes in the Nucleus”, Proceedings of the National Academy of Sciences USA 2002, vol. 99, s. 12246-12251.
- Martin William and Russell Michael J., „On the Origins of Cells: A Hypothesis for the Evolutionary Transitions from Abiotic Geochemistry to Chemoautotrophic Prokaryotes, and from Prokaryotes to Nucleated Cells”, Philosophical Transactions of the Royal Society of London B: Biological Sciences 2003, vol. 358, s. 59-83.
- Mayr Ernst, Systematics and the Origin of Species, Columbia University Press, New York 1944.
- Mayr Ernst, „The Emergence of Evolutionary Novelties”, w: TAX (ed.), The Evolution of Life…, s. 349-380.
- Mcclintock Barbara, „The Origin and Behavior of Mutable Loci in Maize”, Proceedings of the National Academy of Sciences USA 1950, vol. 36, s. 344-355.
- Mcgeoch Adam T. and Bell Stephen D., „Extra-Chromosomal Elements and the Evolution of Cellular DNA Replication Machineries”, Nature Reviews Molecular Cell Biology 2008, vol. 9, s. 569-574.
- Mcinerney James O., „The Causes of Protein Evolutionary Rate Variation”, Trends in Ecology and Evolution 2006, vol. 21, s. 230-232.
- Mclysaght Aoife, Hokamp Karsten, and Wolfe Kenneth H., „Extensive Genomic Duplication During Early Chordate Evolution”, Nature Genetics 2002, vol. 31, s. 200-204.
- Medina Mónica, „Genomes, Phylogeny, and Evolutionary Systems Biology”, Proceedings of the National Academy of Sciences USA 2005, vol. 102, suppl. 1, s. 6630-6635.
- Mendell Jennifer E., Clements Kendall D., Choat J. Howard, and Angert Esther R., „Extreme Polyploidy in a Large Bacterium”, Proceedings of the National Academy of Sciences USA 2008, vol. 105, s. 6730-6734.
- Merchant Sabeeha S., Prochnik Simon E., Vallon Olivier, Harris Elizabeth H., Karpowicz Steven J., Witman George B., Terry Astrid, Salamov Asaf, Fritz-Laylin Lilian K., MAréchal-Drouard Laurence et al., „The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions”, Science 2007, vol. 318, s. 245-250.
- Miereżkowski Konstantin, „Uber Natur und Ursprung der Chromatophoren im Pflanzenreiche”, Biologisches Centralblatt 1905, bd. 25, s. 593-604.
- Miller David J. and Ball Eldon E., „Cryptic Complexity Captured: The Nematostella Genome Reveals Its Secrets”, Trends in Genetics 2008, vol. 24, s. 1-4.
- Mirkin Boris G., Fenner Trevor I., Galperin Michael Y., and Koonin Eugene V., „Algorithms for Computing Parsimonious Evolutionary Scenarios for Genome Evolution, the Last Universal Common Ancestor and Dominance of Horizontal Gene Transfer in the Evolution of Prokaryotes”, BMC Evolutionary Biology 2003, vol. 3, no. 2.
- Molina Nacho and Van Nimwegen Erik, „The Evolution of Domain-Content in Bacterial Genomes”, Biology Direct 2008, vol. 3, no. 51.
- Mushegian Arcady R., „Gene Content of Luca, the Last Universal Common Ancestor”, Frontiers in Bioscience 2008, vol. 13, s. 4657-4666.
- Mushegian Arcady R. and Koonin Eugene V., „Gene Order Is Not Conserved in Bacterial Evolution”, Trends in Genetics 1996, vol. 12, s. 289-290.
- Nelson Karen E., Clayton Rebecca A., Gill Steven R., Gwinn Michelle L., Dodson Robert J., Haft Daniel H., Hickey Erin K., Peterson Jeremy D., Nelson William C., Ketchum Karen A. et al., „Evidence for Lateral Gene Transfer Between Archaea and Bacteria from Genome Sequence of Thermotoga maritima”, Nature 1999, vol. 399, s. 323-329.
- Nierman William C., Eisen Jonathan A., Fleischmann Robert D., and Fraser Claire M., „Genome Data: What Do We Learn?”, Current Opinion in Genetics and Development 2000, vol. 10, s. 343-348.
- Nikoh Naruo, Tanaka Kohjiro, Shibata Fukashi, Kondo Natsuko Ito, Hizume Masahiro, Shimada Masakazu, and Fukatsu Takema, „Wolbachia Genome Integrated in an Insect Chromosome: Evolution and Fate of Laterally Transferred Endosymbiont Genes”, Genome Research 2008, vol. 18, s. 272-280.
- Nosenko Tetyana and Bhattacharya Debashish, „Horizontal Gene Transfer in Chromalveolates”, BMC Evolutionary Biology 2007, vol. 7, no. 173.
- Novichkov Pavel S., Wolf Yuri I., Dubchak Inna, and Koonin Eugene V., „Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes”, Journal of Bacteriology 2009, vol. 191, s. 65-73.
- Ochman Howard and Moran Nancy A., „Genes Lost and Genes Found: Evolution of Bacterial Pathogenesis and Symbiosis”, Science 2001, vol. 292, s. 1096-1099.
- Ohno Susumu, Evolution by Gene Duplication, Springer-Verlag, Berlin — Heidelberg — New York 1970.
- Ohta Tomoko and Gillespie John H., „Development of Neutral and Nearly Neutral Theories”, Theoretical Population Biology 1996, vol. 49, s. 128-142.
- O’Malley Maureen A. and Boucher Yan, „Paradigm Change in Evolutionary Microbiology”, Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 2005, vol. 36, s. 183-208.
- Orgel Leslie and Crick Francis H., „Selfish DNA: The Ultimate Parasite”, Nature 1980, vol. 284, s. 604-607.
- Pace Norman R., „A Molecular View of Microbial Diversity and the Biosphere”, Science 1997, vol. 276, s. 734-740.
- Pace Norman R., „Time for a Change”, Nature 2006, vol. 441, s. 289.
- Pagel Mark and Pomiankowski Andrew, (eds.), Evolutionary Genomics and Proteomics, Sinauer Associates, Inc., Sunderland, Massachusetts 2008.
- Pál Csaba, Papp Balázs, and Hurst Laurence D., „Highly Expressed Genes in Yeast Evolve Slowly”, Genetics 2001, vol. 158, s. 927-931.
- Pál Csaba, Papp Balázs, and Lercher Martin J., „An Integrated View of Protein Evolution”, Nature Reviews Genetics 2006, vol. 7, s. 337-348.
- Panopoulou Georgia, Hennig Steffen, Groth Detlef, Krause Antje, Poustka Albert J., Herwig Ralf, Vingron Martin, and Lehrach Hans, „New Evidence for Genome-Wide Duplications at the Origin of Vertebrates Using an Amphioxus Gene Set and Completed Animal Genomes”, Genome Research 2003, vol. 13, s. 1056-1066.
- Park Jung Woo and Graveley Brenton R., „Complex Alternative Splicing”, Advances in Experimental Medicine and Biology 2007, vol. 623, s. 50-63.
- Pereto Juli, Lopez-Garcia Purificacion, and Moreira David, „Ancestral Lipid Biosynthesis and Early Membrane Evolution”, Trends in Biochemical Sciences 2004, vol. 29, s. 469-477.
- Perna Nicole T., Plunkett III Guy, Burland Valerie, Mau Bob, Glasner Jeremy D., Rose Debra J., Mayhew George F., Evans Peter S., Gregor Jason, Kirkpatrick Heather A. et al., „Genome Sequence of Enterohaemorrhagic Escherichia coli O157:H7”, Nature 2001, vol. 409, s. 529-533.
- Petrusewicz Kazimierz (red.), Teoria ewolucji w wypisach, Wiedza Powszechna, Warszawa 1959.
- Pheasant Michael and Mattick John S., „Raising the Estimate of Functional Human Sequences”, Genome Research 2007, vol. 17, s. 1245-1253.
- Piriyapongsa Jittima, Rutledge Mark T., Patel Sanil, Borodovsky Mark, and Jordan I. King, „Evaluating the Protein Coding Potential of Exonized Transposable Element Sequences”, Biology Direct 2007, vol. 2, no. 31.
- Polavarapu Nalini, Mariño-Ramírez Leonardo, Landsman David, McDonald Jonh F., and Jordan I. King, „Evolutionary Rates and Patterns for Human Transcription Factor Binding Sites Derived from Repetitive DNA”, BMC Genomics 2008, vol. 9, no. 226.
- Poole Anthony M. and Penny David, „Eukaryote Evolution: Engulfed by Speculation”, Nature 2007, vol. 447, s. 913.
- Poole Anthony M. and Penny David, „Evaluating Hypotheses for the Origin of Eukaryotes”, BioEssays 2007, vol. 29, s. 74-84.
- Prangishvili David, Garrett Roger A., and Koonin Eugene V., „Evolutionary Genomics of Archaeal Viruses: Unique Viral Genomes in the Third Domain of Life”, Virus Research 2006, vol. 117, s. 52-67.
- Putnam Nicholas H., Srivastava Mansi, Hellsten Uffe, Dirks Bill, Chapman Jarrod, Salamov Asaf, Terry Astrid, Shapiro Harris, Lindquist Erika A., Kapitonov Vladimir V. et al., „Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization”, Science 2007, vol. 317, s. 86-94.
- Ranea Juan A.G., Grant Alastair, Thornton Janet M., and Orengo Christine A., „Microeconomic Principles Explain an Optimal Genome Size in Bacteria”, Trends in Genetics 2005, vol. 21, s. 21-25.
- Rivera Maria C. and Lake James A., „The Ring of Life Provides Evidence for a Genome Fusion Origin of Eukaryotes”, Nature 2004, vol. 431, s. 152-155.
- Rogers Matthew B., Watkins Russell F., Harper James T., Durnford Dion G., Gray Michael W., and Keeling Patrick J., „A Complex and Punctate Distribution of Three Eukaryotic Genes Derived by Lateral Gene Transfer”, BMC Evolutionary Biology 2007, vol. 7, no. 89.
- Rogozin Igor B., Wolf Yuri I., Sorokin Alexander V., Mirkin Boris G., and Koonin Eugene V., „Remarkable Interkingdom Conservation of Intron Positions and Massive, Lineage-Specific Intron Loss and Gain in Eukaryotic Evolution”, Current Biology 2003, vol. 13, s. 1512-1517.
- Rokas Antonis and Carroll Sean B., „Bushes in the Tree of Life”, PLoS Biology 2006, vol. 4, e352.
- Rose Michael R. and Oakley Todd H., „The New Biology: Beyond the Modern Synthesis”, Biology Direct 2007, vol. 2, no. 30.
- Roy Scott W., „Intron-Rich Ancestors”, Trends in Genetics 2006, vol. 22, s. 468-471.
- Roy Scott W. and Gilbert Walter, „The Evolution of Spliceosomal Introns: Patterns, Puzzles and Progress”, Nature Reviews Genetics 2006, vol. 7, s. 211-221.
- Sagan Lynn, „On the Origin of Mitosing Cells”, Journal of Theoretical Biology 1967, vol. 14, s. 255-274.
- SAwyer Stanley A., Parsch John, Zhang Zhi, and Hartl Daniel L., „Prevalence of Positive Selection Among Nearly Neutral Amino Acid Replacements in Drosophila”, Proceedings of the National Academy of Sciences USA 2007, vol. 104, s. 6504-6510.
- Scannell Devin R., Butler Geraldine, and Wolfe Kenneth H., „Yeast Genome Evolution — The Origin of the Species”, Yeast 2007, vol. 24, s. 929-942.
- Scannell Devin R. and Wolfe Kenneth H., „A Burst of Protein Sequence Evolution and a Prolonged Period of Asymmetric Evolution Follow Gene Duplication in Yeast”, Genome Research 2008, vol. 18, s. 137-147.
- Schneiker Susanne, Perlova Olena, Kaiser Olaf, Gerth Klaus, Alici Aysel, Altmeyer Matthias O., Bartels Daniela, Bekel Thomas, Beyer Stefan, Bode Edna et al., „Complete Genome Sequence of the Myxobacterium Sorangium cellulosum”, Nature Biotechnolology 2007, vol. 25, s. 1281-1289.
- Sémon Marie and Wolfe Kenneth H., „Consequences of Genome Duplication”, Current Opinion in Genetics and Development 2007, vol. 17, s. 505-512.
- She Qunxin, Singh Rama K., Confalonieri Fabrice, Zivanovic Yvan, Allard Ghislaine, Awayez Mariana J., Chan-Weiher Christina C.-Y., Clausen Ib Groth, Curtis Bruce A., De Moors Anick et al., „The Complete Genome of the Crenarchaeon Sulfolobus solfataricus P2”, Proceedings of the National Academy of Sciences USA 2001, vol. 98, s. 7835-7840.
- Simpson George Gaylord, Tempo and Mode in Evolution, Columbia University Press, New York 1944.
- Snel Berend, Bork Peer, and Huynen Martjin A., „Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content”, Genome Research 2002, vol. 12, s. 17-25.
- Soltis Douglas E., Bell Charles D., Kim Sangtae, and Soltis Pamela S., „Origin and Early Evolution of Angiosperms”, Annals of the New York Academy of Sciences 2008, vol. 1133, s. 3-25.
- Sorek Rotem, Shamir Ron, and AST Gil, „How Prevalent Is Functional Alternative Splicing in the Human Genome?”, Trends in Genetics 2004, vol. 20, s. 68-71.
- Srivastava Mansi, Begovic Emina, Chapman Jarrod, Putnam Nicholas H., Hellsten Uffe, Kawashima Takeshi, Kuo Alan, Mitros Therese, Salamov Asaf, Carpenter Meredith L. et al., „The Trichoplax Genome and the Nature of Placozoans”, Nature 2008, vol. 454, s. 955-960.
- Swain Amanda and Coffin John M., „Mechanism of Transduction by Retroviruses”, Science 1992, vol. 255, s. 841-845.
- Syvanen Michael, „Molecular Clocks and Evolutionary Relationships: Possible Distortions Due to Horizontal Gene Flow”, Journal of Molecular Evolution 1987, vol. 26, s. 16-23.
- Syvanen Michael and Kado Clarence I. (eds.), Horizontal Gene Transfer, Academic Press, San Diego 2002.
- Takahata Naoyuki, „On the Overdispersed Molecular Clock”, Genetics 1987, vol. 116, s. 169-179.
- Tax Sol (ed.), The Evolution of Life: Evolution After Darwin, vol. 1, University of Chicago Press, Chicago 1959.
- Tax Sol and Callender Charles (eds.), Evolution After Darwin: The University of Chicago Centennial, University of Chicago Press, Chicago 1960.
- Thomas Charlie A., Jr., „The Genetic Organization of Chromosomes”, Annual Review of Genetics 1971, vol. 5, s. 237-256.
- Tillier Elisabeth R. and Collins Richard A., „Genome Rearrangement by Replication-Directed Translocation”, Nature Genetics 2000, vol. 26, s. 195-197.
- Tobiason Deborah M. and Seifert H. Steven, „The Obligate Human Pathogen, Neisseria gonorrhoeae, Is Polyploid”, PLoS Biology 2006, vol. 4, e185.
- Tringe Susannah G., Von Mering Christian, Kobayashi Arthur, Salamov Asaf A., Chen Kevin, Chang Hwai W., Podar Mircea, Short Jay M., Mathur Eric J., Detter J. Chris et al., „Comparative Metagenomics of Microbial Communities”, Science 2005, vol. 308, s. 554-557.
- Tuskan Gerald A., Difazio Stephen, Jansson Stefan, Bohlmann J., Grigoriev Igor, Hellsten Uffe, Putnam Nicholas, Ralph S., Rombauts Stephane, Salamov Asaf et al., „The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)”, Science 2006, vol. 313, s. 1596-1604.
- Ulrich Luke E., Koonin Eugene V., and Zhulin Igor B., „One-Component Systems Dominate Signal Transduction in Prokaryotes”, Trends in Microbiology 2005, vol. 13, s. 52-56.
- Van Nimwegen Erik, „Scaling Laws in the Functional Content of Genomes”, Trends in Genetics 2003, vol. 19, s. 479-484.
- Van Nimwegen Erik, „Scaling Laws in the Functional Content of Genomes”, w: Koonin, Wolf, and Karev (eds.), Power Laws…, s. 236-253.
- Wagner Andreas, „Robustness, Evolvability, and Neutrality”, FEBS Letters 2005, vol. 579, s. 1772-1778.
- Wagner Gunte P., Amemiya Chris, and Ruddle Frank, „Hox Cluster Duplications and the Opportunity for Evolutionary Novelties”, Proceedings of the National Academy of Sciences USA 2003, vol. 100, s. 14603-14606.
- Wallace Alfred R., „O dążności odmian do nieograniczonego odbiegania od typu pierwotnego”, przeł. Kazimierz Szarski, w: Petrusewicz (red.), Teoria ewolucji w wypisach…, s. 81-91.
- Wallace Alfred R., „On the Tendency of Species to Form Varieties; And on the Perpetuation of Varieties and Species by Natural Means of Selection. III. On the Tendency of Varieties to Depart Indefinitely from the Original Type”, Journal of the Proceedings of the Linnean Society of London 1858, vol. 3, s. 53-62.
- Wellner Alon, Lurie Mor N., and Gophna Uri, „Complexity, Connectivity, and Duplicability as Barriers to Lateral Gene Transfer”, Genome Biology 2007, vol. 8, s. R156.
- Wilson Allan C., Carlson Steven S., and White Thomas J., „Biochemical Evolution”, Annual Review of Biochemistry 1977, vol. 46, s. 573-639.
- Woese Carl R., „Bacterial Evolution”, Microbiological Reviews 1987, vol. 51, s. 221-271.
- Woese Carl R., „There Must Be a Prokaryote Somewhere: Microbiology’s Search for Itself”, Microbiological Reviews 1994, vol. 58, s. 1-9.
- Woese Carl R., „The Universal Ancestor”, Proceedings of the National Academy of Sciences USA 1998, vol. 95, s. 6854-6859.
- Woese Carl R. and Fox George E., „Phylogenetic Structure of the Prokaryotic Domain: The Primary Kingdoms”, Proceedings of the National Academy of Sciences USA 1977, vol. 74, s. 5088-5090.
- Woese Carl R., Kandler Otto, and Wheelis Mark L., „Towards a Natural System of Organisms: Proposal for the Domains Archaea, Bacteria, and Eucarya”, Proceedings of the National Academy of Sciences USA 1990, vol. 87, s. 4576-4579.
- Woese Carl R., Magrum Linda J., and Fox George E., „Archaebacteria”, Journal of Molecular Evolution 1978, vol. 11, s. 245-251.
- Wolf Maxim Y., Wolf Yuri I., and Koonin Eugene V., „Comparable Contributions of Structural-Functional Constraints and Expression Level to the Rate of Protein Sequence Evolution”, Biology Direct 2008, vol. 3, no. 40.
- Wolf Yuri I., Carmel Liran, and Koonin Eugene V., „Unifying Measures of Gene Function and Evolution”, Proceedings of the Royal Society of London B: Biological Sciences 2006, vol. 273, s. 1507-1515.
- Wolf Yuri I., Rogozin Igor B., Grishin Nick V., and Koonin Eugene V., „Genome Trees and the Tree of Life”, Trends in Genetics 2002, vol. 18, s. 472-479.
- Wolfe Kenneth H. and Shields Denis C., „Molecular Evidence for an Ancient Duplication of the Entire Yeast Genome”, Nature 1997, vol. 387, s. 708-713.
- Wright Sewall, Evolution: Selected Papers, University of Chicago Press, Chicago 1986.
- Xiong Yue and Eickbush Thomas H., „Origin and Evolution of Retroelements Based Upon Their Reverse Transcriptase Sequences”, EMBO Journal 1990, vol. 9, s. 3353-3362.
- Yampolsky Lev Y., Kondrashov Fyodor A., and Kondrashov Alexey S., „Distribution of the Strength of Selection Against Amino Acid Replacements in Human Proteins”, Human Molecular Genetics 2005, vol. 14, s. 3191-3201.
- Yooseph Shibu, Sutton Granger, Rusch Douglas B., Halpern Aaron L., Williamson Shannon J., Remington Karin, Eisen Jonathan A., Heidelberg Karla B., Manning Gerard, LI Weizhong et al., „The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families”, PLoS Biology 2007, vol. 5, e16.
- Yutin Natalya, Makarova Kira S., Mekhedov Sergey L., Wolf Yuri I., and Koonin Eugene V., „The Deep Archaeal Roots of Eukaryotes”, Molecular Biology and Evolution 2008, vol. 25, s. 1619-1630.
- Zhang Jianzhi, „Frequent False Detection of Positive Selection by the Likelihood Method with Branch-Site Models”, Molecular Biology and Evolution 2004, vol. 21, s. 1332-1339.
- Zuckerkandl Emile, „Why So Many Noncoding Nucleotides?: The Eukaryote Genome as an Epigenetic Machine”, Genetica 2002, vol. 115, s. 105-129.
- Zuckerkandl Emile and Pauling Linus, „Evolutionary Divergence and Convergence in Proteins”, w: Bryson and Vogel (eds.), Evolving Gene and Proteins…, s. 97-166.
- Zuckerkandl Emile and Pauling Linus, „Molecular Disease, Evolution and Genic Hetero-Geneity”, w: Kasha and Pullman (eds.), Horizons in Biochemistry…, s. 189-225.