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Slide #1. Using Evolution to Explore the Human Genome Slide #2. Comparing genomes Slide #3. The most evolutionarily conserved regions in the human genome don’t code for proteins Slide #4. One of these regulatory elements, 225Kb upstream of DACH1 Slide #5. Genome distribution of all ultra-conserved elements Slide #6. Evolutionary Origins of the Ultra conserved elements Slide #7. Here is an element specific to mammals and birds in the tumor suppressor gene ST7, ¾ of which includes an alt-spliced exon that destroys frame Slide #8. Genome-wide comparative sequence analysis suggests that about 5% of the human genome may be under purifying selection. Slide #9. Grand challenge of human molecular evolution Slide #10. Models of molecular evolution Slide #11. Models of molecular evolution Slide #12. Models of molecular evolution Slide #13. Models of molecular evolution Slide #14. Models of molecular evolution Slide #15. Models of molecular evolution Slide #16. Continuous-time Markov models of Slide #17. Phylogenetic HMMs: models of coding exon evolution Slide #18. Phylogenetic Exon Prediction Slide #19. Some complexities of genome evolution: retrotransposons Slide #20. Processed pseudogenes are (mostly) dead copies of genes inserted occasionally by retrotransposon machinery Slide #21. Inversions, segmental duplications, and large scale translocations Slide #22. Reconstructing Evolutionary History Slide #23. Method for reconstructing ancestral bases Slide #24. Tests of model by simulation Slide #25. Percentage of bases incorrectly reconstructed (from simulated data) Slide #26. 15-20 species are needed to get an accurate reconstruction of the Boreoeutherian genome Slide #27. Reconstruction of about 1Mb of ancestral sequence in CFTR region using real data from 18 species Slide #28. Reconstruction of a segment containing the relic of a MER20 transposon Slide #29. Grand challenge of human Slide #30. Credits Slide #31. The most conserved elements in the genome