Evolutionary Genome Biology

1. Evolutionary Genome Biology Gabor T. Marth, D.Sc. Department of Biology, Boston College marth@bc.edu Medical Genomics Course – Debrecen, Hungary, May 2006

2. Lecture overview 1. Inter-species evolution and comparative genomics 2. Intra-species evolution, population genomics, and human origins

3. 1. Inter-species evolution and comparative genomics Initial sequencing and comparative analysis of the mouse genome Mouse Genome Sequencing Consortium Nature 420, 520-562. 2002

4. Questions of Evolutionary Biology • What are the taxological relationships between living organisms (which organisms are more or less closely related to each other)? • How do genes evolve? • How do genomes evolve? • How do comparisons with other organisms help us understand our own genome?

5. Mechanisms of molecular evolution

6. DNA sequence evolution: mutations

7. Phylogenetic relationships (1) Higgs and Attwood, Bioinformatics and Molecular Evolution, Blackwell Publishing Multiple alignment of mammalian mitochondrial small subunit rRNA sequences

8. Phylogenetic relationships (2) Higgs and Attwood, Bioinformatics and Molecular Evolution, Blackwell Publishing Jukes-Cantor distance matrix for mammalian mitochondrial small subunit rRNA sequences

9. Phylogenetic relationships (3) Higgs and Attwood, Bioinformatics and Molecular Evolution, Blackwell Publishing Phylogenetic tree constructed from mammalian mitochondrial small subunit rRNA sequences

10. Gene structure evolution: duplications

11. Gene duplication – paralogs Lander et al. Initial sequencing and analysis of the human genome, Nature, 2001

12. Evolution of chromosome organization

13. Synteny Initial sequencing and comparative analysis of the mouse genome Mouse Genome Sequencing Consortium Nature 420, 520-562. 2002

14. Gene classes across organisms Lander et al. Initial sequencing and analysis of the human genome, Nature, 2001

15. Gene conservation across organisms Lander et al. Initial sequencing and analysis of the human genome, Nature, 2001

16. Comparative genomics helps gene annotations

17. 2. Intra-species evolution, population genomics, and human origins

18. Questions about human evolution • How do we discover / assess genetic variations? • What is the level of diversity across humans? • How can we model the ancestral and mutation processes? • What do phylogenetic analyses of human mitochondrial sequences tell us about human origins and dispersal? • Does mitochondrial DNA give us the full picture? • What do we learn from model-fitting analysis of nuclear DNA? • A single wave of out-of-Africa migration or multiple waves?

19. look at multiple sequences from the same genome region • use base quality values to decide if mismatches are true polymorphisms or sequencing errors How do we discover SNPs?

20. 1. Fragment recruitment (database search) 2. Anchored alignment 3. Paralog identification 4. SNP detection SNP discovery procedure genome reference sequence

21. genome reference EST WGS BAC ~ 8 million Sachidanandam et al. Nature 2001 SNP discovery on the genome scale

22. Human genetic diversity average polymorphism rate between a pair of human chromosomes: 1 SNP in 1,300 bp of sequence polymorphism density along chromosomes varies widely

23. What explains heterogeneity? G+C nucleotide content CpG di-nucleotide content recombination rate 3’ UTR 5.00 x 10-4 5’ UTR 4.95 x 10-4 Exon, overall 4.20 x 10-4 Exon, coding 3.77 x 10-4 synonymous 366 / 653 non-synonymous 287 / 653 functional constraints Variance is so high that these quantities are poor predictors of nucleotide diversity in local regions hence random processes are likely to govern the basic shape of the genome variation landscape  (random) genetic drift

24. TAACAAT • mutations are propagated down through generations MRCA TAAAAAT TAAAAAT TAACAAT TAAAAAT TAAAAAT TAACAAT TAACAAT TAACAAT • and determine present-day variation patterns The origin of genetic variations • sequence variations are the result of mutation events TAAAAAT

25. acggttatgtaga acggttatgtaga acggttatgtaga accgttatgtaga acggttatgtaga acggttatgtaga accgttatgtaga acggttatgtaga acggttatgtaga accgttatgtaga Recombination messes up phylogenies accgttatgtaga accgttatgtaga acggttatgtaga • because of recombination, DNA sequences may not have a unique common ancestor, hence phylogenetic analysis may not apply

26. What does mtDNA say about human origins? However, the mitochondrion is only a single locus (~16kb, short on the scale of the 3Gb human genome) Campbell and Heyer. Genomics, Proteomics, Bioinformatics. Cummings.

27. What does nuclear DNA say? • Because of recombination, phylogenetic analysis is not feasible (there is not a unique tree that can explain the ancestry of DNA sequences) • Instead, one uses statistical “genetic analysis” i.e. one examines the statistical properties of the possible ancestries that produced the nucleotide sequences observed in individuals

28. 2. allele frequency spectrum (AFS): distribution of SNPs according to allele frequency in a set of samples “common” “rare” Polymorphism data 1. marker density (MD): distribution of number of SNPs in pairs of sequences

29. Population genetic models bottleneck stationary collapse expansion past history present MD (simulation) AFS (direct form)

30. Data fitting: polymorphism density • best model is a bottleneck shaped population size history N3=11,000 N2=5,000 T2=400 gen. N1=6,000 T1=1,200 gen. present Marth et al. PNAS 2003 • our conclusions from the marker density data are confounded by the unknown ethnicity of the public genome sequence we looked at allele frequency data from ethnically defined samples

31. model consensus: bottleneck N3=10,000 N2=2,000 T2=400 gen. N1=20,000 T1=3,000 gen. present Data fitting: allele frequency bottleneck ~ 3,000 generations (or 100,000 years) ago

32. bottleneck modest but uninterrupted expansion Data from other human populations European data African data Marth et al. Genetics 2004

33. What nuclear DNA tells us our results Recent African Origin Multiregional