Eugene Koonin for Knowledge Stream
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Eugene Koonin for Knowledge Stream

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31 октября самый цитируемый ученый русского происхождения, известный эволюционный биолог Евгений Кунин рассказал в Digital October о постмодернистском взгляде на эволюционные процессы.......

31 октября самый цитируемый ученый русского происхождения, известный эволюционный биолог Евгений Кунин рассказал в Digital October о постмодернистском взгляде на эволюционные процессы.

http://digitaloctober.ru/ru/events/knowledge_stream_evolyutsiya_po_sluchayu

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  • 1. Information Comparative genomics rewrites evolution textbooks: a “postmodern synthesis” of Evolutionary Biology? Eugene V. Koonin National Center for Biotechnology Information, NLM, NIH, Bethesda, Maryland, USA Moscow, Digital October, 31/10/2013
  • 2. Information The Modern Synthesis
  • 3. Information Nothing in biology makes sense except in the light of evolution Evolutionary process represented as change in allele frequency driven by natural selection
  • 4. Information The beginnings of comparative genomes Haemophilus influenzae Mycoplasma genitalium Venter et al. 1995
  • 5. Information
  • 6. Exponential accumulation of prokaryotic genome sequences 1000 Information No. of Sequenced Genomes 100 10 Bacteria Archaea 1 7/3/1995 7/2/1997 7/2/1999 7/1/2001 7/1/2003 Date 6/30/2005 6/30/2007
  • 7. 0% Thermotoga maritima MSB8 Treponema pallidum subsp. pallidum str. Nichols Leptospira interrogans serovar Copenhageni str. Fiocruz L1-… Pseudomonas aeruginosa PAO1 Escherichia coli K12 Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough Burkholderia mallei ATCC 23344 Agrobacterium tumefaciens str. C58 Pirellula sp. Fusobacterium nucleatum subsp. nucleatum ATCC 25586 Mesoplasma florum L1 Clostridium acetobutylicum ATCC 824 Lactococcus lactis subsp. lactis Il1403 Bacillus subtilis subsp. subtilis str. 168 Solibacter usitatus Ellin6076 Thermus thermophilus HB27 Deinococcus radiodurans R1 Prochlorococcus marinus subsp. marinus str. CCMP1375 Anabaena variabilis ATCC 29413 Synechocystis sp. PCC 6803 Dehalococcoides ethenogenes 195 Candidatus Protochlamydia amoebophila UWE25 Chlamydia muridarum Nigg Chlorobium tepidum TLS Salinibacter ruber DSM 13855 Bacteroides thetaiotaomicron VPI-5482 Aquifex aeolicus VF5 Bifidobacterium longum NCC2705 Streptomyces coelicolor A3(2) Mycobacterium tuberculosis H37Rv Nanoarchaeum equitans Kin4-M Thermoplasma volcanium GSS1 Pyrococcus horikoshii OT3 Methanopyrus kandleri AV19 Methanosarcina acetivorans C2A Methanocaldococcus jannaschii DSM 2661 Methanothermobacter thermautotrophicus str. Delta H Halobacterium sp. NRC-1 Archaeoglobus fulgidus DSM 4304 Aeropyrum pernix K1 Information Most (~70-80%) of genes in prokaryotic genomes are evolutionarily conserved –belong to COGs – orthologous lineages - distinct units of evolution 100% 90% 80% 70% 60% 50% 40% 30% 20% 10%
  • 8. Information Understanding evolution in the light of comparative genomics and systems biology: Is there a „postmodern synthesis‟ in sight?
  • 9. Postmodern reassessment of some central propositions of Darwin and the Modern Synthesis Postmodern status The material for evolution is provided, primarily, by random, heritable variation (random local mutations, in modern terms). Information Proposition Only partly true. The repertoire of relevant changes greatly expanded to include duplication of Fixation of (rare) beneficial changes by natural selection is the main driving force of evolution. Only partly true. Natural (positive) selection is important but is only one of several fundamental factors of evolution and is not quantitatively dominant. Neutral processes combined with purifying selection dominate evolution, and direct effects of environmental cues on the genome {(quasi)Lamarckian phenomena] are important as well. The variations fixed by natural selection are “infinitesimally small”. Evolution adheres to gradualism. False. Even single gene duplications and HGT of single genes are by no means “infinitesimally small” let alone deletion or acquisition of larger regions, genome rearrangements, whole-genome duplication, and most dramatically, endosymbiosis. Gradualism is not the principal regime of evolution. Uniformitarianism: evolutionary processes remained, largely, the same throughout the evolution of life. Only partly true. Present day evolutionary processes were important since the origin of replication. However, major transitions in the evolution like the origin of eukaryotes could be brought about by (effectively) unique events such as endosymbiosis, and the earliest stages of evolution (pre-LUCA) partially relied on distinct processes not involved in subsequent, “normal” evolution. genes, genome regions, and entire genomes; loss of genes and, generally, genetic material; HGT including massive gene flux in cases of endosymbiosis; invasion of mobile selfish elements and recruitment of sequences from them; and more. More importantly, (quasi)directed, Lamarckian variation is recognized as a major factor of evolution.
  • 10. Information The 3 modalities of evolution Koonin, Wolf, Biol. Direct 2009
  • 11. Information NATURE REVIEWS | MICR OBIOLOGY VOLUME 9 | JUNE 2011 | 467
  • 12. Information Makarova et al. Nature Rev Microbiol 2011
  • 13. Information CRISPR/Cas: a case of bona fide Lamarckian evolution …although elements of stochasticity and selection are always present Koonin, Wolf, Biol. Direct 2009
  • 14. Lamarck’s gift to biotechnology Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012 Aug 17;337(6096):816-21 Information Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. Multiplex genome engineering using CRISPR/Cas systems.Science. 2013 Feb 15;339(6121):819-23 Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science. 2013 Feb 15;339(6121):823-6. Brouns SJ. Molecular biology. A Swiss army knife of immunity. Science. 2012 Aug 17;337(6096):808-9 Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. Genome engineering using the CRISPR-Cas9 system. Nat Protoc. 2013 Nov;8(11):2281-308
  • 15. Diverse Lamarckian and quasi-Lamarckian phenomena Phenomenon Biological role/function Phyletic spread Lamarckian criteria Genomic changes caused by environmental factor Bona fide Lamarckian Most of the Yes Archaea and many bacteria Changes are specific to relevant genomic loci Changes provide adaptation to the causative factor Yes Yes Information CRISPR/Cas Defense against viruses and other mobile elements piRNA Defense against transposable elements in germline Animals Yes Yes Yes HGT (specific cases) Adaptation to new environment, stress response, resistance Yes Yes HGT (general phenomenon) Diverse innovations No Yes/no Stress-induced mutagenesis Stress response/resistance/ adaptation to new conditions Archaea, Yes bacteria, unicellular eukaryotes Quasi-Lamarckian Archaea, Yes bacteria, unicellular eukaryotes Ubiquitous Yes No or partially Yes (but general evolvability enhanced as well) Koonin, Wolf, Biol. Direct 2009
  • 16. Postmodern reassessment of some central propositions of Darwin and the Modern Synthesis Postmodern status The material for evolution is provided, primarily, by random, heritable variation. Information Proposition Only partly true. The repertoire of relevant random changes greatly expanded to include duplication of genes, genome regions, and entire genomes; loss of genes and, generally, genetic material; HGT including massive gene flux in cases of endosymbiosis; invasion of mobile selfish elements and recruitment of sequences from them; and more. More importantly, (quasi)directed (Lamarckian) variation is recognized as a major factor of evolution. The variations fixed by natural selection are “infinitesimally small”. Evolution strictly adheres to gradualism. False. Even single gene duplications and HGT of single genes are by no means “infinitesimally Uniformitarianism: evolutionary processes remained, largely, the same throughout the evolution of life. Only partly true. Present day evolutionary processes were important since the origin of replication. However, major transitions in the evolution like the origin of eukaryotes could be brought about by (effectively) unique events such as endosymbiosis, and the earliest stages of evolution (pre-LUCA) partially relied on distinct processes not involved in subsequent, “normal” evolution. small” let alone deletion or acquisition of larger regions, genome rearrangements, whole-genome duplication, and most dramatically, endosymbiosis. Gradualism is not the principal regime of evolution.
  • 17. The recurrent structure in the gene universe reflects dramatic genome plasticity – extensive loss and gain of genes - at all levels 10000 Shell Core Cloud 1000 Shell Core: ~70 Shell: ~5700 100 Cloud DATA Number of COGs 1000 Number of COGs Core Cloud: ~24000 10000 DATA 100 10 Information 10 1 1 0 50 100 150 200 250 300 350 0 400 338 Archaea and Bacteria 10000 DATA Core Accessory genome Cloud Shell Number of COGs 1000 Core genome 100 10 1 0 5 10 15 20 25 30 35 40 45 Number of Organisms 44 Escherichia and Salmonella 5 10 15 20 25 30 35 40 45 Number of Organisms Number of Organisms 50 41 Archaea Fractal (self-similar) structure of the prokaryotic gene space Tripartite organization of pangenomes at all levels – major differences in gene repertoires Koonin, Logic of Chance 2011
  • 18. 1960-1990 PARADIGM SHIFT: from GENOMES TO PANGENOMES Information 1990-2010 2010-2020 16S RNA Genomes Pangenomes
  • 19. Information Open (unlimited growth) vs closed pan-genome
  • 20. Information Mathematical modeling of pangenome evolution reveals closed pangenomes and exponential growth of estimated pangenome size with tree depth Lobkovsky, Wolf, Koonin, in preparation (Only) a million proteins for molecular biologists?
  • 21. Postmodern reassessment of some central propositions of Darwin and the Modern Synthesis Postmodern status The material for evolution is provided, primarily, by random, heritable variation. Information Proposition Only partly true. The repertoire of relevant random changes greatly expanded to include duplication of The variations fixed by natural selection are “infinitesimally small”. Evolution adheres to gradualism. False. Even single gene duplications and HGT of single genes are by no means “infinitesimally small” let alone deletion or acquisition of larger regions, genome rearrangements, whole-genome duplication, and most dramatically, endosymbiosis. Gradualism is not the principal regime of evolution. Fixation of (rare) beneficial changes by natural selection is the main driving force of evolution. True only to a small extent. Natural (positive) selection is important but is only one of Uniformitarianism: evolutionary processes remained, largely, the same throughout the evolution of life. Only partly true. Present day evolutionary processes were important since the origin of replication. However, major transitions in the evolution like the origin of eukaryotes could be brought about by (effectively) unique events such as endosymbiosis, and the earliest stages of evolution (pre-LUCA) partially relied on distinct processes not involved in subsequent, “normal” evolution. genes, genome regions, and entire genomes; loss of genes and, generally, genetic material; HGT including massive gene flux in cases of endosymbiosis; invasion of mobile selfish elements and recruitment of sequences from them; and more. More importantly, (quasi)directed (Lamarckian) variation is recognized as a major factor of evolution. several fundamental factors of evolution and is not quantitatively dominant. Neutral processes combined with purifying selection dominate evolution, and direct effects of environmental cues on the genome - (quasi)Lamarckian phenomena - are important as well. Universal patterns of evolution seem to emerge without natural selection
  • 22. Information The 3 modalities of evolution Koonin, Wolf, Biol. Direct 2009
  • 23. Selection and drift in classic population genetics drift+selection – small Ne Information Sewall Wright (1889-1988) Selection - large Ne
  • 24. Non-adaptive evolution of genomic complexity Nothing makes sense in evolution except in light of population genetics Lynch M. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci U S A. 2007 Lynch M, Conery JS. The origins of genome complexity. Science. 2003 Nov 21;302(5649):1401-4. Information Complete genomic sequences from diverse phylogenetic lineages reveal notable increases in genome complexity from prokaryotes to multicellular eukaryotes. The changes include gradual increases in gene number, resulting from the retention of duplicate genes, and More abrupt increases in the abundance of spliceosomal introns and mobile genetic elements. We argue that many of these modifications emerged passively in response to the long-term population-size reductions that accompanied increases in organism size. According to this model, much of the restructuring of eukaryotic genomes was initiated by nonadaptive processes, and this in turn provided novel substrates for the secondary evolution of phenotypic complexity by natural selection. The enormous long-term effective population sizes of prokaryotes may impose a substantial barrier to the evolution of complex genomes and morphologies.
  • 25. Information Estimates of the composite parameter Neu for a phylogenetically diverse assemblage of species M Lynch, J S Conery Science 2003;302:1401-1404 Published by AAAS
  • 26. Information The major intrusion of stochasticity into Biology: do statistical laws rule Life?
  • 27. Information Some key universals of genome/molecular phenome evolution Karev et al. 2002; Jordan et al. 2004; Lobkovsky, Wolf, Koonin, 2010; Koonin, Wolf 2010
  • 28. The major intrusion of stochasticity into Biology: do statistical laws rule Life? PLoS Comput Biol. 2011 Aug;7(8):e1002173. Are there laws of genome evolution? Information Koonin EV. Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the evolutionary rates of orthologous genes; the power law-like distributions of paralogous family size and node degree in various biological networks; the negative correlation between a gene's sequence evolution rate and expression level; and differential scaling of functional classes of genes with genome size. The universals of genome evolution can be accounted for by simple mathematical models similar to those used in statistical physics, such as the birth-death-innovation model. These models do not explicitly incorporate selection; therefore, the observed universal regularities do not appear to be shaped by selection but rather are emergent properties of gene ensembles. Although a complete physical theory of evolutionary biology is inconceivable, the universals of genome evolution might qualify as "laws of evolutionary genomics“ in the same sense "law" is understood in modern physics.
  • 29. Information Laws and generative models in evolutionary genomics Koonin, PLOS Comp Biol 2011
  • 30. A general physical principle behind all universals? Shannon entropy: H= - pilogpi Max(H) – most random, least unexpected distribution MaxEnt Principle: the probability distribution of any variable in a large ensemble of data/measurements tends to the distribution with Max(H) within the applicable constraints Information S Frank SA. The common patterns of nature J Evol Biol. 2009; 22:1563-85 E. T. Jaynes Karev, Koonin: Parabolic Replicator Dynamics and the Principle of Minimum Tsallis Information Gain. Biology Direct 2013 The results of this analysis show that the general MaxEnt principle is the underlying law for the evolution of a broad class of replicator systems including not only exponential but also parabolic and hyperbolic systems.
  • 31. Postmodern reassessment of some central propositions of Darwin and the Modern Synthesis Postmodern status The material for evolution is provided, primarily, by random, heritable variation. Information Proposition Only partly true. The repertoire of relevant random changes greatly expanded to include duplication of genes, genome regions, and entire genomes; loss of genes and, generally, genetic material; HGT including massive gene flux in cases of endosymbiosis; invasion of mobile selfish elements and recruitment of sequences from them; and more. More importantly, (quasi)directed (Lamarckian) variation is recognized as a major factor of evolution. Fixation of (rare) beneficial changes by natural selection is the main driving force of evolution. Only partly true. Natural (positive) selection is important but is only one of several fundamental factors of evolution and is not quantitatively dominant. Neutral processes combined with purifying selection dominate evolution, and direct effects of environmental cues on the genome {(quasi)Lamarckian phenomena] are important as well. The variations fixed by natural selection are “infinitesimally small”. Evolution adheres to gradualism. False. Even single gene duplications and HGT of single genes are by no means “infinitesimally small” let alone deletion or acquisition of larger regions, genome rearrangements, whole-genome duplication, and most dramatically, endosymbiosis. Gradualism is not the principal regime of evolution. Uniformitarianism: evolutionary processes remained, largely, the same throughout the evolution of life. Only partly true. Present day evolutionary processes were important since the origin of replication. However, major transitions in the evolution like the origin of eukaryotes could be brought about by (effectively) unique events such as endosymbiosis, and the earliest stages of evolution (pre-LUCA) partially relied on distinct processes not involved in subsequent, “normal” evolution.
  • 32. Information “Amitochondrial” eukaryotes “In the mid-1990s, a somewhat pedestrian view of eukaryotic origins, the 'archezoa hypothesis', held sway. This maintained that a protoeukaryote (with nucleus) engulfed the mitochondrial ancestor. Supporting the theory were 'archezoa', anaerobic eukaryotes with no mitochondria. Archezoa apparently populated the oldest branches of the eukaryote tree, suggesting that eukaryotes began diversifying before mitochondria entered the picture.” Poole, Penny, Nature 447, 913 (21 June 2007)
  • 33. Information There are no (known) true amitochondrial eukaryotes Animal mitochondrion Hydrogenosome from an anaerobic fungus Mitosomes from Giardia Van der Giezen, Tovar. Degenerate mitochondria. EMBO Rep. 2005 Jun;6(6):525-30. All “archezoa” possess: -mitochondrial genes in nuclear genomes -degenerate derivatives of mitochondria They are not archezoa at all!
  • 34. “Symbiotic” hypotheses Information “Archezoan” hypotheses ???? Hypotheses on the origin of eukaryotes Embley, Martin, Nature 2006
  • 35. Information Adaptation to survive the intron invasion Origin of nucleus and spliceosome Dispersal of introns, population bottleneck Non-adaptive process – Attack on the host genome Unidirectional flow of genes and introns from symbiont to host – ratchet due to propagation/lysis of symbiont Invasion 2 prokaryotes: archaeon and a-proteobacterium Martin, Koonin, 2006, Introns and the origin of nucleus-cytosol compartmentalization. Nature 440: 41-5
  • 36. Information The proposed chain of causes and effects in eukaryogenesis – the pivotal roles of mitochondrial endosymbiosis and intron invasion Koonin, The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate? Biol Direct. 2006 Aug 14;1:22
  • 37. Postmodern reassessment of some central propositions of Darwin and the Modern Synthesis Postmodern status Evolution by natural selection tends to produce increasingly complex adaptive features of organisms; hence progress as a general trend in evolution. Information Proposition False. Genomic complexity probably evolved as a “genomic syndrome” caused by weak purifying The entire evolution of life can be depicted as a single “big tree”. False. The discovery of the fundamental contributions of HGT and mobile genetic elements to genome evolution invalidate the TOL concept in its original sense. However, trees remain essential templates to represent evolution of individual genes and many phases of evolution in groups of relatively close organisms. The possibility of salvaging the TOL as a central trend of evolution remains. All extant cellular life forms descend from very few, and probably, one ancestral form (LUCA). True. Comparative genomics leaves no doubt of the common ancestry of cellular life. However, it also yields indications that LUCA(S) might have been very different from modern cells. selection in small population and not as an adaptation. There is no consistent trend towards increasing complexity in evolution, and the notion of evolutionary progress is unwarranted.
  • 38. Non-adaptive evolution of genomic complexity Nothing makes sense in evolution except in light of population genetics Lynch M. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci U S A. 2007 Lynch M, Conery JS. The origins of genome complexity. Science. 2003 Nov 21;302(5649):1401-4. Information Complete genomic sequences from diverse phylogenetic lineages reveal notable increases in genome complexity from prokaryotes to multicellular eukaryotes. The changes include gradual increases in gene number, resulting from the retention of duplicate genes, and More abrupt increases in the abundance of spliceosomal introns and mobile genetic elements. We argue that many of these modifications emerged passively in response to the long-term population-size reductions that accompanied increases in organism size. According to this model, much of the restructuring of eukaryotic genomes was initiated by nonadaptive processes, and this in turn provided novel substrates for the secondary evolution of phenotypic complexity by natural selection. The enormous long-term effective population sizes of prokaryotes may impose a substantial barrier to the evolution of complex genomes and morphologies.
  • 39. Information There is no general trend toward increasing complexity in evolution… actually, the opposite might be true
  • 40. Information Reconstruction of archaeal genome evolution: reduction prevails Wolf YI, Makarova KS, Yutin N, Koonin EV. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. Biol Direct. 2012 Dec 14;7:46
  • 41. Information Maximum Likelihood (MCMC) reconstruction of intron gain/loss during eukaryote evolution from comparativegenomic analysis of 100 genomes (mean/median+ confidence intervals) •Pronounced excess of loss over gain: mostly a story of decreasing complexity •Intron-rich ancestors •Human-like intron-density in Last Eukaryotic Common Ancestor (LECA) •No intron-poor stage from LECA to mammals – no stage of intense purifying selection Csuros, Rogozin Koonin, PLOS Comp Biol 2011
  • 42. log complexity Information Punctuated model of evolution: long phases of reduction punctuated by bursts time Wolf, Koonin, BioEssays 2013
  • 43. Postmodern reassessment of some central propositions of Darwin and the Modern Synthesis Postmodern status Evolution by natural selection tends to produce increasingly complex adaptive features of organisms; hence progress as a general trend in evolution. Information Proposition False. Genomic complexity probably evolved as a “genomic syndrome” caused by weak purifying selection in small population and not as an adaptation. There is no consistent trend towards increasing complexity in evolution, and the notion of evolutionary progress is unwarranted. The entire evolution of life can be depicted as a single “big tree”. False. The discovery of the fundamental contributions of HGT and mobile genetic elements to All extant cellular life forms descend from very few, and probably, one ancestral form (LUCA). True. Comparative genomics leaves no doubt of the common ancestry of cellular life. However, it also yields indications that LUCA(S) might have been very different from modern cells. genome evolution invalidate the TOL concept in its original sense. However, trees remain essential templates to represent evolution of individual genes and many phases of evolution in groups of relatively close organisms. The possibility of salvaging the TOL as a central trend of evolution remains.
  • 44. A brief history of TOL Information Thinking of the history of life in terms of phylogenetic trees is as old as scientific biology (if not older) Charles Darwin (1859) Origin of Species [one and only illustration]: "descent with modification" Ernst Haeckel (1879) The Evolution of Man
  • 45. A brief history of TOL Information Advent of molecular phylogenetics – expectations of objectively reconstructed complete Tree of Life Carl R. Woese (1928-2012) Woese et al. (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. PNAS 87, 4576-4579 [Figure 1, modified]
  • 46. “Forest of Life” to replace Tree of Life Puigbò P, Wolf YI, Koonin EV. Information Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol. 2009;8(6):59 0.5 0.4 0.3 1 0.2 2 0.1 3 4 0 -0.6 -0.4 -0.2 -0.1 -0.2 -0.3 -0.4 -0.5 0 0.2 0.4 0.6 0.8 5 6 7 NUTs
  • 47. Horizontal gene flow dominates evolution, at least in prokaryotes d’ =0 d’ = (d-Dr) / (Ds-Dr) d’=1 NUTs Information 0.63 +/- 0.35 Dr d’=1 Ds Dr = 0.67 Ds > Dr d’ = 1 – ((d-Ds) / (Dr-Ds)) d’=0 FOL Ds Ds < Dr Dr 0.39 +/- 0.31 Dr = 0.67 TNT (Tree/Net Trend): scoring tree-like and netlike evolution quantitatively 0: Network(green) – Neutral (black) – 1:Tree (red) Puigbo, Wolf, Koonin, Genome Biol Evol 2010
  • 48. Postmodern reassessment of some central propositions of Darwin and the Modern Synthesis Postmodern status Evolution by natural selection tends to produce increasingly complex adaptive features of organisms; hence progress as a general trend in evolution. Information Proposition False. Genomic complexity probably evolved as a “genomic syndrome” caused by weak purifying selection in small population and not as an adaptation. There is no consistent trend towards increasing complexity in evolution, and the notion of evolutionary progress is unwarranted. The entire evolution of life can be depicted as a single “big tree”. False. The discovery of the fundamental contributions of HGT and mobile genetic elements to genome evolution invalidate the TOL concept in its original sense. However, trees remain essential templates to represent evolution of individual genes and many phases of evolution in groups of relatively close organisms. The possibility of salvaging the TOL as a central trend of evolution remains. All extant cellular life forms descend from very few, and probably, one ancestral form (LUCA). True. Comparative genomics leaves no doubt of the common ancestry of cellular life. However, it also yields indications that LUCA(S) might have been very different from modern cells.
  • 49. LUCA: undeniable but elusive Information ~100 universally conserved protein and RNA genes = primarily translation system components Koonin EV. Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol. 2003
  • 50. Information Mulkidjanian AY, Bychkov AY, Dibrova DV, Galperin MY, Koonin EV. Origin of first cells at terrestrial, anoxic geothermal fields. Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):E821-30
  • 51. CRISPR spacer acquisition direct adaptation resistance plasmid acquisition strong selection horizontal gene transfer deterministic intermediate selection stress-induced mutagenesis draft genome streamlining degradation ratchet transposition-induced weak Junk shuffling selection accumulation/ gene duplication complexification gene loss drift random mutation random generation of variation fixation of variation/mode of genome evolution random Information determini stic From randomness to determinism: evolution spans the whole range
  • 52. Information The biosphere as the world of viruses
  • 53. Viruses are the dominant entities in the biosphere – physically and genetically – as shown by viral metagenomics – virome studies 1 cm3 of seawater contains 106-109 virus particles Information Suttle, C.A. (2005) Nature 437:356 There are millions of diverse bacteriophage species in the water, soil, and gut Edwards and Rohwer (2005) Nat. Rev. Microbiol. 3:504 •Viruses are the most abundant biological entities in the biosphere: there are 10-100 virus particles per cell •The pangenomes of viruses and cellular organisms have [at least] comparable complexities
  • 54. Information Some of the largest viruses host their own parasites La Scola et al. The virophage as a unique parasite of the giant mimivirus. Nature. 2008 Sep 4;455(7209):100-4
  • 55. Information Philippe et al. Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes Science 19 July 2013: Vol. 341 no. 6143 pp. 281-286
  • 56. Information (At least) two independent origins of giant viruses: Pandoraviruses appear to be highly derived Phycodnaviruses Smaller, simpler common ancestor(?) Mimi Yutin, Koonin. Biol. Direct 2013 Pandora
  • 57. Information The ancient Virus World •Viruses and virus-like genetic elements are not “just” pathogens: they are dominant entities in the biosphere •Emergence of virus-like parasites is inevitable in any replicating system •In the pre-cellular epoch, the genetic elements that later became viral and cellular genomes comprised a single pool in which they mixed, matched, and evolved new, increasingly complex gene ensembles •Different replication strategies including RNA replication, reverse transcription, and DNA replication evolved already in the primordial genetic pool •With the emergence of prokaryotic cells, a distinct pool of viral genes formed that retained its identity ever since as evidenced by the extant distribution of viral hallmark genes: “virus world” or the virosphere •The emergence of the eukaryotic cell was a second melting pot of virus evolution, from which viruses of eukaryotes originated via recombination of genes from prokaryote viruses, retroelements, and the evolving eukaryotic host •Viruses make essential contributions to the evolution of the genomes of cellular life forms, in particular, as vehicles of HGT: GTAs, transducing phages Koonin EV, Senkevich TG, Dolja VV. The ancient Virus World and evolution of cells. Biol Direct. 2006
  • 58. viroids Information dsDNA viruses ssDNA viruses Retroviruses/ elements dsRNA viruses (+)RNA viruses Koonin, Logic of Chance 2011 Bacteria KEukaryota Archaea (-)RNA viruses Virus Empire Cellular Empire
  • 59. Virus World constructive neutral evolution of complexity Selfish gene HGT phylogeno mics Neutral theory Quantitative laws and physical principles of evolution Population genetics Quantitative theory of selection and drift Darwinian theory of natural selection evolution of evolvabilit y Information Neo-Lamarckian evolution models Lamarckian L'influence des circonstances Modified from: Koonin EV, Wolf YI. Evolution of microbes and viruses: a paradigm shift in evolutionary biology? Front Cell Infect Microbiol. 2012;2:119
  • 60. Information FT Press; 1 edition (September 10, 2011) Marine Corps marathon 2011, Washington, DC
  • 61. Information Acknowledgments Bill Martin Valerian Dolja Didier Raoult