Structural and Evolutionary Genomics NATURAL SELECTION IN GENOME EVOLUTION Giorgio Bernardi

1. Structural and Evolutionary Genomics NATURAL SELECTION IN GENOME EVOLUTION Giorgio Bernardi SZN ELSEVIER

2. Formation of the earth Multicellular organisms Origin of life Big Bang CONSCIOUSNESS & CULTURE BRAIN LIFE COSMOS SZN -14 -10 -5 0 Billions years A vision of reality N. Hartmann’s “strata of existence” (after Bernardi, 2005)

3. SZN Origin of life • Absolutely exceptional chance event (Jacques Monod, 1970) • Necessary event under the prevailing physico-chemical conditions (Christian de Duve, 1995)

4. SZN Jacques Monod “Le Hasard et la Nécessité” 1970

5. Christian de Duve “Vital Dust: Life as a Cosmic Imperative” 1995

6. SZN • Georges Cuvier • (1769 – 1832) • Fixity of species • Extinction of species

7. Jean-Baptiste Lamarck “Philosophie Zoologique” 1809 SZN • “Internal force” • Inheritance of acquired characters

8. SZN Alfred R. Wallace “On the Tendency of Varieties toDepart Indefinitely from the Original Type” (1858)

9. SZN Charles Darwin “The Origin of Species” 1859

10. SZN Evolution: descent with modification Charles Darwin

11. SZN Summary • Classical approaches to the study of evolution; classical theories • Our approach: structural and evolutionary genomics • An ultra-darwinian view of evolution: the neo-selectionist theory

12. SZN Approaches to the study of evolution At the level of the “classical phenotype” (form and function of organisms) • at the trait level (natural selection ; Darwin, 1859; Wallace, 1859)

13. SZN Darwin's finches

14. SZN This preservation of favourable individual differences and variations [positive selection], and the destruction of those which are injurious variations [negative selection], I have called Natural Selection, or the Survival of the Fittest [adaptation]. Variations neither useful nor injurious [neutral variations] would not be affected by natural selection and would be left either a fluctuating element, … or would ultimately become fixed, ... Charles Darwin

15. SZN Approaches to the study of evolution At the level of the “classical phenotype” (characters) • at the trait level (natural selection) • at the genetic level (selectionist theory ; Fisher, 1930; Wright, 1931; Haldane, 1932)

16. Ronald A. Fisher John B.S. Haldane Sewall Wright SZN

17. SZN The selectionist (neo-darwinian, synthetic) theory of evolution reconciled Mendel’s laws of inheritance with evolution but neglected neutral changes

18. SZN Approaches to the study of evolution At the level of the “classical phenotype” (proteins and expression) • at the trait level (natural selection) • at the genetic level (selectionist theory) • at the protein level (Zuckerkandl and Pauling, 1962; Sueoka, 1962; Freese, 1962; Kimura, 1968; 1983)

19. Amino acid differences Time (Myr) SZN The molecular clock

20. AT GC PROKARYOTES 25 50 75 GC SZN Biases in the replication machinery Sueoka (1962); Freese (1962)

21. SZN Motoo Kimura “The Neutral Theory of Molecular Evolution” 1983

22. SZN The mutation-random drift theory (the neutral theory) “the main cause of evolutionary change at the molecular level - changes in the genetic material itself - is random fixation of selectively neutral or nearly neutral mutants ”. (Kimura, 1983)

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24. SZN Approaches to the study of evolution At the level of the “genome phenotype” (Bernardi et al., 1973, 1976) Instead of looking at a few genes, this approach looked at the whole genome, more specifically at its compositional patterns and their evolution, moving, therefore, from the genetic level to the genomic level

25. SZN The genome: an operational definition The haploid chromosome set Hans Winkler (1920)

26. SZN • constant amount of DNA per cell in any given organism (Boivin et al., 1948; Mirsky and Ris, 1949) • c-value, or constant value (Swift, 1950) • genome size (Hinegardner, 1976)

27. SZN The prokaryotic paradigm The genome as the sum total of genes

28. SZN Genome size, coding sequences and gene numbers in some representative organisms a in approximate figures b kb, kilobases, or thousands of base pairs, bp; Mb, megabases, or millions of bp; (Gb, gigabases, are billions of base pairs)

29. SZN The genome as the sum total of coding and non-coding sequences

30. The genome The bean bag view Additive vs. cooperative properties The integrated ensemble view SZN

31. SZN Vertebrates • are a very small phylum • have common genetic background (vertebrates share most genes) • have a large genome (~ 3000 Mb; with coding sequences representing < 3%)

32. SZN Structural genomics of vertebrates: our main conclusions ● First evidence that the eukaryotic genome is an integrated ensemble: no junk DNA) ● Incompatibility with neutral theory

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35. Isochore patterns 1 2 1 3 4 5 6 7 Costantini, Saccone, Auletta and Bernardi Pavlicek, Paces, Clay and Bernardi 8 9 10 2004 2001

36. SZN Genome phenotypes DNA Coding Sequences

37. SZN Compositional correlations Universal correlations

38. Hydrophobicity SZN

39. SZN

40. Gene distribution • Bernardi et al., 1984 • Mouchiroud et al., 1991 • Zoubak et al., 1996 • Lander et al., 2001 Correlations with structure and function

41. SZN Genome evolutionin vertebrates • Conservative mode • Transitional mode

42. SZN Genome evolution in vertebrates The conservative mode Mammalian orders are characterized by • a star-like phylogeny (over 100 Myrs) • a strong mutational AT bias (GC  AT; mC  T) • a conservation of base composition, methylation and CpG levels

43. SZN Most recent common ancestor AT bias 100 Myrs Extant mammalian orders similar isochore patterns

44. Genome evolution in vertebrates Cold-blooded Ancestral Genome Core GC increase Genome desert Warm-blooded Genome Core SZN The transitional mode

45. SZN THE COMPOSITIONAL TRANSITIONS:(cold- to warm-blooded vertebrates) Compositional changes • concerned the (gene-dense) ancestral genome core • affected both coding and non-coding sequences (at comparable and correlated levels) • occurred (and were similar) in the independent ancestral lines of mammals and birds (convergent evolution) • did not affect cold-blooded vertebrates (with exceptions) • stopped with the appearance of present-day mammals and birds (an equilibrium was reached)

46. SZN The formation and maintenance of GC-rich isochores is due to NATURAL SELECTION Selective advantages: Increased thermodynamic stability of DNA, RNA & proteins (Bernardi and Bernardi, 1986)

47. 3 Polar fish Tropical/Temperate fish R = 0.50 2 R = 0.45 5mC, % R = 0.80 1 Mammals 5mC, % 0 35 40 45 50 Snakes Lizards Turtles Crocodiles Polar fish GC, % 2 1 Mammals SZN 0 35 40 45 50 GC, % Varriale et al., 2005

48. SZN The compositional transitions affected • only a small part of the genome (the ancestral genome core) • both coding and non coding sequences (at comparable and correlated levels)

49. SZN Chromosomal regions in interphase nuclei Saccone et al., 2002; Di Filippo et al., 2005

50. SZN The genome compartmentalization, the genome phenotype and the genomic code, the conservative and transitional modes of genome evolution cannot be accounted for by “a random fixation of neutral mutants” (i.e., by the neutral theory)