2. Genomfart Any general theory for genome evolution will have to account for: the unique natural history of various genetic elements, the population-genetic forces that promote their proliferation vs. eradication. Prior to invoking natural selection as the determinant of genomic features, we need to understand the power and consequences of nonadaptive forces.

3. Expansion in Gene Number with the Evolution of Multicellularity Cause or Effect? Prokaryotes 500 - 7,000 Urochordata Arthropoda Nematoda 16,000 14,000 21,000 Unicellular sps. Fungi 2,000 – 13,000 5,000 – 10,000 Vertebrata Vascular plants 30,000 – 50,000 25,000 – 60,000

4. Genome complexity arises as a pathological response to small population size and degenerative mutations: Adaptive evolution is a secondary consequence of such complexity. Gene number – preservation of duplicate genes. Spliceosomal (nuclear) intron proliferation. Modular regulatory region complexity. Transposons and retrotransposons.

5. Three Genetic Perils of Evolving Multicellularity (Finlay 2002, Science) Slope  -1.0 Reduction in absolute population size Reduced recombination per physical distance  Increase in the mutation rate  Prokaryotes Vertebrates Invertebrates

6. Nucleotide Variation at Silent Sites 4Nu 1/(2N) 2u2u

7. Factoring out the mutation rate (u) from N e u, Prokaryotes5  10 7 to 2  10 9 Unicellular eukaryotes5  10 6 to 4  10 8 Invertebrates6  10 5 to 2  10 6 Vertebrates30,000 to 100,000 Annual plants 40,000 to 500,000 Trees ~10,000 Approximate Ranges of Effective Population Sizes

8. Phylogenetic Distribution of Spliceosomal Introns

9. Why genes in pieces? Intron Gain, b Intron Loss, d Loss of Coding Function, n s Loss of Intron Function, n

10. Donor site is usually GT; acceptor site is usually AG. An internal branchpoint A is essential for initiation of the splicing reaction. In S. cerevisiae, this region is conserved over a 7-bp stretch (TACTAAC). In most animals, there is a polypyrimidine tract of ~10 nucleotides upstream of the AG-acceptor site. In C. elegans, the 3’ end is usually TTTTCAG. Exon splicing enhancers and silencers are common. Sequence Requirements for Proper pre-mRNA Splicing GU---------------A----Py--AG ESE / ESS

11. The probability of intron fixation declines, while the probability of intron loss increases with increasing population size. Diploid probability of intron fixation = 2s / (e 4Ns – 1) Diploid probability of intron loss = 2s / (1 – e -4Ns ) s = 10 -6 Probability = 1/(2N) 

12. Intron size (bp) decreases with population size. Intron number per gene approaches an asymptotic limit at small N e. Threshold Population Size for Intron Colonization

13. Mean intron number increases with the target size

14. H. sapiens 4 6 10 8 2 Introns overdispersed Introns random Introns tend to be evenly distributed within genes

15. Spliceosome Ribosome Cytoplasm Nucleus NMD

16. Geometry of NMD Fully effective Ineffective Partially effective

17. Evolutionary Novelty Out of Degenerative Mutations One such mechanism may have been intron-dependent nonsense-mediated decay, which would have also promoted the colonization of secondary introns. Once they had sufficiently colonized various eukaryotic lineages, introns provided a reliable substrate for the evolution of new mechanisms of gene processing. Under this model, intron colonization is stabilized once full coverage of a gene is achieved.

18. Mobile Genetic Elements Cut-and-paste, DNA-based: Copy-and-paste, with RNA intermediates:

19. Nu = 0.065 0.015 0.004 Threshold Population Size for Colonization of Mobile Elements

20. The Classical Model for the Fates of Duplicate Genes Duplication Nonfunctionalization (pseudogene) Neofunctionalization

21. Under the classical model, the mean time to duplicate gene loss: is no more than a few million generations, increases with increasing population size. Unlinked Linked Unlinked Linked 1/(2u null )

22. _________________________________________________________________________________ Fraction Date ofHalf Phylogenetic group Surviving Event (MYA)Life Reference _________________________________________________________________________________ Salmonids 0.50 100 100 Allendorf et al. (1975) Catastomid fish(suckers) 0.50 50 50 Ferris and Whitt (1979) Cyprinus carpio (carp) 0.60 12 16 David et al. (2003) Loaches 0.25 28 14 Ferris and Whitt (1977) Arabidopsis thaliana 0.33 50 31 Ermolaeva et al. (2003) Oryza sativa (rice) 0.34 54 35 Vandepoele et al. (2003) Saccharomyces cerevisiae 0.08 100 27 Wolfe and Shields (1997) _________________________________________________________________________________ Long Half-Lives of Duplicate Genes in Polyploid Species

23. head thorax coding region The DDC Model Duplication Degeneration neofunctionalizationnonfunctionalization subfunctionalization Complementation

24. Subfunctionalization is a Common Fate of Duplicate Genes in Metazoans and Vascular Plants Partitioned expression of HoXB1 duplicates in zebrafish embryo hindbrains recapitulates the expression pattern of the single gene in mouse embryos (McClintock et al. 2002) Complementary loss of regulatory elements: HoxB1a HoxB1b Coding-region modifications: Duplicated  -catenin genes inC. eleganspartition cell-signalling and cell-adhesion functions carried out by single gene in flies and vertebrates (Korswagen et al. 2000)

25. Loss of alternative splice sites: Duplicated synapsin genes in Fuguadopted alternative splice variants of single-copy gene in tetrapods (Yu et al. 2003) Sexual specialization: Autosomal MADS-box gene duplicated on to the Y chromosome inSilene latifoliafocuses on expression in stamens relative to single-copy gene in outgroup species (Matsunaga et al. 2003)

26. The Subfunctionalization Model Uniquely Predicts a Decrease in Duplicate-gene Preservation with Increasing N e Unlinked Linked Unlinked Linked Nonfunctionalization Population Size (N) Scaled Proability of Neofunctionalization Subfunctionalization Neofunctionalization

27. The Genomic Distribution of Duplicate Genes

28. The Evolutionary Demography of Duplicate Genes Stable Age Distribution Under a Steady-state Birth-death Process No. of Duplication Events

29. __________________________________________ Homo sapiens0.0049 Mus musculus0.0030 Fugu rubripes0.0043 Drosophila melanogaster0.0011 Anopheles gambiae0.0062 Caenorhabditis elegans0.0028 Plasmodium falciparum0.0003 Saccharomyces cerevisiae0.0025 Schizosaccharomyces pombe0.0016 Encephalitozoon cuniculi0.0118 __________________________________________ Average: 0.0037 (0.0007) Birth Rates of Duplicate Genes (time scale = 1% divergence at silent sites) The rate of duplication per gene is about the same as the rate of mutation per nucleotide site. Incremental gene duplication is sufficient to duplicate an entire genome on a time scale of ~100 Mys.

30. Duplicate Genes Survive Longer in Small Populations

33. Spontaneous Emergence of a Modular Regulatory Region Population size x Mutation rate Probability of Modularization Duplication Modularization Silencing

34. Evolutionary Novelty Out of Degenerative Mutations and Random Genetic Drift Subfunctionalization eliminates pleiotropic constraints unique to single-copy genes. Duplicate-gene preservation buys time for the neofunctionalization process. Small population size promotes the evolution of modularity upon which subfunctionalization depends.

35. The stochastic birth and loss of duplicate genes leads to the passive origin of reproductive isolating barriers by microchromosomal rearrangements.

36. The small population sizes of multicellular species provide an environment that is conducive to the evolution of various types of genomic complexity that are essentially unattainable in unicellular species. No need to invoke selection for genomic streamlining in microbes or for modularity and evolvability in multicellular species. Genome Complexity and Organismal Complexity There is a logical distinction between the nonadaptive forces that initially allow the establishment of genomic complexity and the subsequent ability of natural selection to take advantage of new and reliable forms of gene and genome architecture.