1. Generating Diversity: how genes and genomes evolve Erin “They call me Dr. Worm” Friedman 29 September 2005

2. Intro/Background Why do we care about generating diversity? What exactly is mutation? How does evolution act on mutations? How does evolution work on a molecular scale? It’s not just about frog mating calls…

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4. 09_02_Germ_somatic2.jpg

5. 09_03_altered.genes_part1.jpg Genetic Change  Mutation

6. 09_03_altered.genes_part2.jpg

7. Point Mutations Nucleotide change, addition, deletion Silent Mutation – same AA (synonymous) Sense Mutation – different AA (nonsynonymous) Nonsense Mutation – stop codon (translation termination) Plotkin et. al., Nature 2004

8. Generating Point Mutations Replication Errors (Polymerase isn’t perfect) –Human rate 1 in 10 10 Chemical mutagens or radiation Repair failure after such DNA damage

9. Sickle Cell Anemia Caused by a point mutation in beta chain of hemoglobin (GAG  GTG) Changes glutamic acid to valine –What kind of mutation is this? Autosomal Recessive Disorder Cell morphology http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/M/Mutations.html

10. Sickle Cell Evolution Sickle cell anemia vs. sickle cell trait (het) Low oxygen  Acidity  sickling Link between sickle cell trait and malaria Positive selection for sickle cell trait in some regions with high malaria incidence http://www.nhlbi.nih.gov/health/dci/Diseases/Sca/SCA_WhatIs.html

11. 09_05_Gene.duplicate.jpg Gene duplication / deletion

12. Globin Gene Evolution Especially important in larger, multicellular organisms –Diffusion doesn’t cut it Multiple duplication events Primitive animals have one globin chain; higher vertebrates have two Beta-globin duplicated / mutated again (fetal, adult) and each product duplicated…

13. 09_06_globin.1.jpg Gene duplication / deletion

14. 09_07_globin.2.jpg

15. Duplication  Divergence New gene copy is free to mutate Not all duplications lead to functional new genes (pseudogenes) Impact of gene deletions?

16. 09_09_exon.jpg Exon Duplication

17. Fig. 9-10 Exon Shuffling Recombination between non- homologous genes A few thousand exons could explain protein variability today Combinations of different exon elements (symbols = different protein domains)

18. Exon shuffling Can bacteria use exon duplication / shuffling to form a functional gene? Why would big introns be beneficial for generating diversity in this manner?

19. Transposable Elements Parasitic DNA sequences Can disrupt function, alter regulation, or make new genes by bringing along gene segments with it Inverted repeats Transposase binding domains http://engels.genetics.wisc.edu/Pelements/fig1.html

20. 09_11_exon.arrange.jpg Transposons

21. Transposable Elements in regulatory regions Common human example of gene inactivation from transposon insertion: Factor VIII  hemophilia

22. Transposons as a tool Transposable elements can be used to study particular genes Knock out genes and look for a phenotype (reverse genetics) Drosophila P-Element (transposon) –Can carry different genes, map insertion by phenotype

23. 09_13_conjugation.jpg Horizontal Transfer: organisms exchanging genes

24. Conjugation animation

25. 09_14_promiscuous.jpg

26. Consequences of Horizontal Transfer Gene duplication Rapid evolution Bacterial antibiotic resistance –Some strains of TB are resistant to 9 antibiotics –“Drug resistance may have contributed to the 58 percent rise in infectious disease deaths among Americans between 1980 and 1992.” (Mayo Clinic) –Where in genome would resistance genes live?

27. What Now? We can use this information to reconstruct an evolutionary tree

28. Analyzing Genomes Homologous genes have common ancestry, similar nt sequences –Finding homologues with BLAST Different genome segments evolve differently –Highly conserved / essential genes = constrained Purifying selection removes dysfunctional individuals Positive selection preserves beneficial mutations Genetic Drift: random, unconstrained mutation How we measure mutation rate

29. 09_15_Phylogen.trees.jpg Evolutionary descent

30. 09_16_Ancestral.gene.jpg

31. Why reconstruct ancestor sequences? Can be used to study evolution rates –Why can’t you just compare 2 genes? –Measuring rates with dN/dS, PAML Evolution rate is a good screen for looking for candidate genes (compare gene to ancestor, not to homologous gene): –Some genes likely evolve rapidly (e.g. those involved in infection, defense) –Highly conserved, essential genes likely evolve slowly

32. 09_17_Human_chimp.jpg Conserved synteny

33. Rediers et. al., Microbiology 2004 Sample genome analysis

34. Synteny in Pseudomonas

37. 09_19_human_mouse1.jpg “Junk” DNA Exons more highly conserved than introns: different evolutionary constraints in different parts of genome What kind of selection is acting on the exons? What phenomenon is taking place in the intron?

38. 09_21_Fugu.introns.jpg Introns (noncoding DNA) are non-essential

39. 09_22_genetic.info.jpg Conserved sequences: comparing distant genomes Small subunit of rRNA