1. Genome evolution
There are both proximate and ultimate explanations in molecular biology
Mutation continually generates variation in genome content and structure
Raw material for natural selection
Potential for non-adaptive evolution
Function is too blunt a concept for genome evolution

3. The genome as phenotype
Evolutionary biologists study both pattern and process, or mechanism
What unexpected patterns do we see
Within genomes?
By comparisons among them?
What can we infer about proximal and ultimate mechanisms by
Catching evolution red-handed?
Testing genome evolutionary models?

4. Three open questions
How rapidly do the expression profiles of duplicated genes diverge?
What is the extent of polymorphism in gene order within species?
What is responsible for physical clusters of co-expressed genes?

5. Three open questions
How rapidly do the expression profiles of duplicated genes diverge?
What is the extent of polymorphism in gene order within species?
What is responsible for physical clusters of co-expressed genes?

6. Arabidopsis MPSS With Blake Meyers and Barry Kesner
Massively parallel signature sequencing
Bead based expression monitoring
Estimates for nearly all genes
Estimates are good even at low expression
Sample eight tissues from Arabidopsis thaliana
Couple with genome-wide phylogenetic analysis of duplicated genes

7. Measuring expression distance
Tissue 2
Tissue 1
Tissue 3

8. Measuring duplication age
Rice
Athal1
Athal2 T1 T2

9. Divergence between duplicates
Expression distance
Age of duplication

10. Does the pattern differ for
Tandem duplicates?
Transposed duplicates?
Polyploidy remnants?

11. Three open questions
How rapidly do the expression profiles of duplicated genes diverge?
What is the extent of polymorphism in gene order within species?
What is responsible for physical clusters of co-expressed genes?

12. Gene order polymorphism
With Jason Lieb and Jennifer Kriss
Using high-throughput methods to compare gene order in two yeast strains
One strain known to lack 7 ORFs present in the reference genome
The key ingredients
Comparative genomic hybridization to a whole-genome chip
Whole-genome genotyping in multiple haploid recombinants from a cross between the two strains

13. Comparative genomic hybridization on a chip

14. Detecting gene transposition
Genes that are in different chromosomal positions in the two strains will appear as deletions and amplifications in the recombinant progeny

15. Stay tuned!

16. Three open questions
How rapidly do the expression profiles of duplicated genes diverge?
What is the extent of polymorphism in gene order within species?
What is responsible for physical clusters of co-expressed genes?

17. Natural selection and clusters of co-expressed genes
With Jianhua Hu
Neighboring genes with similar expression profiles are more common than expected in C. elegans
Two classes of explanation
Adaptive: more efficient, less error-prone
Maladaptive: due to recent transpositions

18. Selection and recombination
In regions of low recombination
deleterious mutations can hitch-hike to high frequency along with favorable ones
favorable mutations are kept at low frequency by linkage to deleterious ones
The effectiveness of natural selection is directly related to recombination rate
Are clusters found in regions of high recombination (adaptive) or low (maladaptive)?

19. Measuring the co-expression of neighboring genes
Measure the distance in expression space from central gene to each neighbor
If neighboring genes are co-expressed, the average of these distances will be smaller than for non-neighboring genes d1 d2 d3 d4 X

20. Sizes of co-expressed clusters

21. Measuring recombination rate

22. Expression distance and recombination rate
data:  expdis2 and recrate normal-z = , p-value = alternative hypothesis: true rho is less than 0 sample estimates:         rho  
Spearman = -0.07
p =

23. Opportunities abound!
The field of genome evolution is a vast and open playing field
Gads of genome data
Some seriously cool experimental techniques
A golden age in bioinformatics and molecular evolution